Building DAG of jobs...
Conda environment ../mw-lib/src/snakemake/envs/r_brgenomics.yaml will be created.
Conda environment ../mw-lib/src/snakemake/envs/star.yaml will be created.
Conda environment ../mw-lib/src/snakemake/envs/coreutils.yaml will be created.
Conda environment ../mw-lib/src/snakemake/envs/pygtftk.yaml will be created.
Conda environment ../mw-lib/src/snakemake/envs/deeptools.yaml will be created.
Conda environment ../mw-lib/src/snakemake/envs/sickle.yaml will be created.
Conda environment ../mw-lib/src/snakemake/envs/sra-tools.yaml will be created.
Conda environment ../mw-lib/src/snakemake/envs/bowtie2.yaml will be created.
Incomplete Conda environment ../mw-lib/src/snakemake/envs/deeptools_samtools.yaml will be recreated.
Conda environment ../mw-lib/src/snakemake/envs/samtools.yaml will be created.
Conda environment ../mw-lib/src/snakemake/envs/subread.yaml will be created.
Conda environment ../mw-lib/src/snakemake/envs/igvtools.yaml will be created.
Conda environment ../mw-lib/src/snakemake/envs/ucsc.yaml will be created.
Job counts:
	count	jobs
	1	bowtie2_build
	20	bowtie2_paired_end_extra
	17	bowtie2_single_end_extra
	15	cat
	27	deepTools_bamCoverage_extra
	928	deepTools_computeMatrix_SingleBw_extra
	140	deepTools_computeMatrix_extra
	2133	deepTools_plotHeatmap_extra
	10	deepTools_spikeIn_bamCoverage
	1	gtftk_convert_ensembl
	12	gtftk_coverage_extra_chrominfo_bed_bw
	8	gtftk_coverage_extra_chrominfo_bed_single_bw
	1	gtftk_get_5p_3p_coords
	1	gtftk_select_by_key_key_value
	31	gunzip_extra
	4	igvtools_tdftobedgraph
	87	ln_alias
	58	ln_srf_parent_dir
	1	meta_broad_tall_rev3_q4
	1	meta_broad_tall_rev3_q4_single
	1	meta_broad_tall_rev3_q4_spikein_single
	1	r_compute_pausing_index
	1	r_compute_pausing_index_from_our_rnaseq
	1	r_extract_control_sharp_subsets_from_Atak2013
	1	r_extract_control_sharp_subsets_from_our_rnaseq
	33	samtools_index
	20	samtools_sam_to_bam_bai_extra
	27	samtools_sort_extra
	27	samtools_view_sam_to_bam_extra
	15	sickle_pe_extra
	18	sickle_se_extra
	16	sort_extra
	16	sra_tools_fastq_dump_se_extra
	1	star_build_index
	5	star_pe_extra
	1	star_se_extra
	2	subread_featureCounts_extra
	4	tail_extra
	1	tar_xvzf_igenome
	4	ucsc_bedGraphToBigWig
	32	wget_protocol
	3723

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L001_R2_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L001_R2_001.fastq.gz
    jobid: 3613
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L001_R2_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L001_R2_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L001_R2_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L001_R2_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L002_R2_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L002_R2_001.fastq.gz
    jobid: 3630
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L002_R2_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L002_R2_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L002_R2_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L002_R2_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_EC_TH91_H3K4me3_S010NDH1.bed
    output: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_EC_TH91_H3K4me3_S010NDH1.bed
    jobid: 2352
    reason: Missing output files: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_EC_TH91_H3K4me3_S010NDH1.bed
    wildcards: filler=mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_EC_TH91_H3K4me3_S010NDH1.bed

ln -srf '../mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_EC_TH91_H3K4me3_S010NDH1.bed' 'out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_EC_TH91_H3K4me3_S010NDH1.bed'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L001_R1_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L001_R1_001.fastq.gz
    jobid: 3617
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L001_R1_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L001_R1_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L001_R1_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L001_R1_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L003_R1_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L003_R1_001.fastq.gz
    jobid: 3627
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L003_R1_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L003_R1_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L003_R1_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L003_R1_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L004_R2_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L004_R2_001.fastq.gz
    jobid: 3616
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L004_R2_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L004_R2_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L004_R2_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L004_R2_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L003_R1_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L003_R1_001.fastq.gz
    jobid: 3577
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L003_R1_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L003_R1_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L003_R1_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L003_R1_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: /gpfs/projects/spicuglia/mw/inp/fastq/202010026_R335_SS/fastq/Run_336_B/S003889_17_H3K4me3_LOUCY_PBIT_24H_1.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3_1.fastq.gz
    jobid: 3468
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3_1.fastq.gz
    wildcards: id=sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3_1.fastq.gz
    priority: 10

ln -srf '/gpfs/projects/spicuglia/mw/inp/fastq/202010026_R335_SS/fastq/Run_336_B/S003889_17_H3K4me3_LOUCY_PBIT_24H_1.fastq.gz' out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3_1.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L001_R1_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L001_R1_001.fastq.gz
    jobid: 3575
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L001_R1_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L001_R1_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L001_R1_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L001_R1_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/blueprint/ChIP-Seq/ERS663696/ERR770348/ERR770348.fastq.gz
    output: out/ln/updir/mw/inp/fastq/blueprint/ChIP-Seq/ERS663696/ERR770348/ERR770348.fastq.gz
    jobid: 3684
    reason: Missing output files: out/ln/updir/mw/inp/fastq/blueprint/ChIP-Seq/ERS663696/ERR770348/ERR770348.fastq.gz
    wildcards: filler=mw/inp/fastq/blueprint/ChIP-Seq/ERS663696/ERR770348/ERR770348.fastq.gz

ln -srf '../mw/inp/fastq/blueprint/ChIP-Seq/ERS663696/ERR770348/ERR770348.fastq.gz' 'out/ln/updir/mw/inp/fastq/blueprint/ChIP-Seq/ERS663696/ERR770348/ERR770348.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: /gpfs/projects/spicuglia/mw/inp/fastq/202010026_R335_SS/fastq/Run_336_B/S003886_14_H3K4me3_JURKAT_PBIT_24H_1.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3_1.fastq.gz
    jobid: 3462
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3_1.fastq.gz
    wildcards: id=sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3_1.fastq.gz
    priority: 10

ln -srf '/gpfs/projects/spicuglia/mw/inp/fastq/202010026_R335_SS/fastq/Run_336_B/S003886_14_H3K4me3_JURKAT_PBIT_24H_1.fastq.gz' out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3_1.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_Jurkat.bed
    output: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_Jurkat.bed
    jobid: 2205
    reason: Missing output files: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_Jurkat.bed
    wildcards: filler=mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_Jurkat.bed

ln -srf '../mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_Jurkat.bed' 'out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_Jurkat.bed'

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: /gpfs/projects/spicuglia/mw/inp/fastq/202010026_R335_SS/fastq/Run_336_B/S003887_15_H3K4me3_LOUCY_DMSO_24H_2.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3_2.fastq.gz
    jobid: 3465
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3_2.fastq.gz
    wildcards: id=sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3_2.fastq.gz
    priority: 10

ln -srf '/gpfs/projects/spicuglia/mw/inp/fastq/202010026_R335_SS/fastq/Run_336_B/S003887_15_H3K4me3_LOUCY_DMSO_24H_2.fastq.gz' out/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3_2.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD4_TH91_H3K4me3_S010R5H1.bed
    output: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD4_TH91_H3K4me3_S010R5H1.bed
    jobid: 3314
    reason: Missing output files: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD4_TH91_H3K4me3_S010R5H1.bed
    wildcards: filler=mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD4_TH91_H3K4me3_S010R5H1.bed

ln -srf '../mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD4_TH91_H3K4me3_S010R5H1.bed' 'out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD4_TH91_H3K4me3_S010R5H1.bed'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L003_R2_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L003_R2_001.fastq.gz
    jobid: 3623
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L003_R2_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L003_R2_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L003_R2_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L003_R2_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: /gpfs/projects/spicuglia/mw/inp/fastq/202010026_R335_SS/fastq/Run_336_B/S003884_12_H3K4me3_JURKAT_DMSO_24H_1.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3_1.fastq.gz
    jobid: 3458
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3_1.fastq.gz
    wildcards: id=sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3_1.fastq.gz
    priority: 10

ln -srf '/gpfs/projects/spicuglia/mw/inp/fastq/202010026_R335_SS/fastq/Run_336_B/S003884_12_H3K4me3_JURKAT_DMSO_24H_1.fastq.gz' out/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3_1.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L002_R1_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L002_R1_001.fastq.gz
    jobid: 3618
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L002_R1_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L002_R1_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L002_R1_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L002_R1_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L001_R2_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L001_R2_001.fastq.gz
    jobid: 3629
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L001_R2_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L001_R2_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L001_R2_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L001_R2_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_LC_TH91_H3K4me3_S010Q7H1.bed
    output: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_LC_TH91_H3K4me3_S010Q7H1.bed
    jobid: 2360
    reason: Missing output files: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_LC_TH91_H3K4me3_S010Q7H1.bed
    wildcards: filler=mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_LC_TH91_H3K4me3_S010Q7H1.bed

ln -srf '../mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_LC_TH91_H3K4me3_S010Q7H1.bed' 'out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_LC_TH91_H3K4me3_S010Q7H1.bed'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L004_R1_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L004_R1_001.fastq.gz
    jobid: 3628
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L004_R1_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L004_R1_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L004_R1_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L004_R1_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: /gpfs/projects/spicuglia/mw/inp/fastq/202010026_R335_SS/fastq/Run_336_B/S003888_16_H3K4me3_LOUCY_PBIT_5H_2.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3_2.fastq.gz
    jobid: 3467
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3_2.fastq.gz
    wildcards: id=sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3_2.fastq.gz
    priority: 10

ln -srf '/gpfs/projects/spicuglia/mw/inp/fastq/202010026_R335_SS/fastq/Run_336_B/S003888_16_H3K4me3_LOUCY_PBIT_5H_2.fastq.gz' out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3_2.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run204/S002104_Loucy_PBIT_24h_10uM-72078/Loucy-PBIT-24h-10uM_S7_L003_R1_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run204/S002104_Loucy_PBIT_24h_10uM-72078/Loucy-PBIT-24h-10uM_S7_L003_R1_001.fastq.gz
    jobid: 3643
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run204/S002104_Loucy_PBIT_24h_10uM-72078/Loucy-PBIT-24h-10uM_S7_L003_R1_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run204/S002104_Loucy_PBIT_24h_10uM-72078/Loucy-PBIT-24h-10uM_S7_L003_R1_001.fastq.gz

ln -srf '../mw/inp/fastq/run204/S002104_Loucy_PBIT_24h_10uM-72078/Loucy-PBIT-24h-10uM_S7_L003_R1_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run204/S002104_Loucy_PBIT_24h_10uM-72078/Loucy-PBIT-24h-10uM_S7_L003_R1_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD8_TH91_H3K4me3_S010S3H1.bed
    output: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD8_TH91_H3K4me3_S010S3H1.bed
    jobid: 2362
    reason: Missing output files: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD8_TH91_H3K4me3_S010S3H1.bed
    wildcards: filler=mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD8_TH91_H3K4me3_S010S3H1.bed

ln -srf '../mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD8_TH91_H3K4me3_S010S3H1.bed' 'out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD8_TH91_H3K4me3_S010S3H1.bed'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L003_R1_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L003_R1_001.fastq.gz
    jobid: 3611
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L003_R1_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L003_R1_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L003_R1_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L003_R1_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: /gpfs/projects/spicuglia/mw/inp/fastq/202010026_R335_SS/fastq/Run_336_B/S003884_12_H3K4me3_JURKAT_DMSO_24H_2.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3_2.fastq.gz
    jobid: 3459
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3_2.fastq.gz
    wildcards: id=sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3_2.fastq.gz
    priority: 10

ln -srf '/gpfs/projects/spicuglia/mw/inp/fastq/202010026_R335_SS/fastq/Run_336_B/S003884_12_H3K4me3_JURKAT_DMSO_24H_2.fastq.gz' out/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3_2.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L003_R2_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L003_R2_001.fastq.gz
    jobid: 3631
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L003_R2_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L003_R2_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L003_R2_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L003_R2_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run204/S002104_Loucy_PBIT_24h_10uM-72078/Loucy-PBIT-24h-10uM_S7_L002_R1_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run204/S002104_Loucy_PBIT_24h_10uM-72078/Loucy-PBIT-24h-10uM_S7_L002_R1_001.fastq.gz
    jobid: 3642
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run204/S002104_Loucy_PBIT_24h_10uM-72078/Loucy-PBIT-24h-10uM_S7_L002_R1_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run204/S002104_Loucy_PBIT_24h_10uM-72078/Loucy-PBIT-24h-10uM_S7_L002_R1_001.fastq.gz

ln -srf '../mw/inp/fastq/run204/S002104_Loucy_PBIT_24h_10uM-72078/Loucy-PBIT-24h-10uM_S7_L002_R1_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run204/S002104_Loucy_PBIT_24h_10uM-72078/Loucy-PBIT-24h-10uM_S7_L002_R1_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_EC_TH91_H3K4me3_S010NDH1.bed
    output: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_EC_TH91_H3K4me3_S010NDH1.bed
    jobid: 3316
    reason: Missing output files: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_EC_TH91_H3K4me3_S010NDH1.bed
    wildcards: filler=mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_EC_TH91_H3K4me3_S010NDH1.bed

ln -srf '../mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_EC_TH91_H3K4me3_S010NDH1.bed' 'out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_EC_TH91_H3K4me3_S010NDH1.bed'

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: /gpfs/projects/spicuglia/mw/inp/fastq/202010026_R335_SS/fastq/Run_336_B/S003885_13_H3K4me3_JURKAT_PBIT_5H_1.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3_1.fastq.gz
    jobid: 3460
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3_1.fastq.gz
    wildcards: id=sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3_1.fastq.gz
    priority: 10

ln -srf '/gpfs/projects/spicuglia/mw/inp/fastq/202010026_R335_SS/fastq/Run_336_B/S003885_13_H3K4me3_JURKAT_PBIT_5H_1.fastq.gz' out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3_1.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L004_R1_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L004_R1_001.fastq.gz
    jobid: 3636
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L004_R1_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L004_R1_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L004_R1_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L004_R1_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_LC_TH91_H3K4me3_S010Q7H1.bed
    output: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_LC_TH91_H3K4me3_S010Q7H1.bed
    jobid: 3315
    reason: Missing output files: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_LC_TH91_H3K4me3_S010Q7H1.bed
    wildcards: filler=mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_LC_TH91_H3K4me3_S010Q7H1.bed

ln -srf '../mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_LC_TH91_H3K4me3_S010Q7H1.bed' 'out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_LC_TH91_H3K4me3_S010Q7H1.bed'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L003_R2_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L003_R2_001.fastq.gz
    jobid: 3581
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L003_R2_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L003_R2_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L003_R2_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L003_R2_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L002_R2_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L002_R2_001.fastq.gz
    jobid: 3614
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L002_R2_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L002_R2_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L002_R2_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L002_R2_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L004_R1_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L004_R1_001.fastq.gz
    jobid: 3578
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L004_R1_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L004_R1_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L004_R1_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L004_R1_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: /gpfs/projects/spicuglia/mw/inp/fastq/202010026_R335_SS/fastq/Run_336_B/S003889_17_H3K4me3_LOUCY_PBIT_24H_2.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3_2.fastq.gz
    jobid: 3469
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3_2.fastq.gz
    wildcards: id=sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3_2.fastq.gz
    priority: 10

ln -srf '/gpfs/projects/spicuglia/mw/inp/fastq/202010026_R335_SS/fastq/Run_336_B/S003889_17_H3K4me3_LOUCY_PBIT_24H_2.fastq.gz' out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3_2.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD8_TH91_H3K4me3_S010S3H1.bed
    output: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD8_TH91_H3K4me3_S010S3H1.bed
    jobid: 2356
    reason: Missing output files: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD8_TH91_H3K4me3_S010S3H1.bed
    wildcards: filler=mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD8_TH91_H3K4me3_S010S3H1.bed

ln -srf '../mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD8_TH91_H3K4me3_S010S3H1.bed' 'out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD8_TH91_H3K4me3_S010S3H1.bed'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L002_R2_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L002_R2_001.fastq.gz
    jobid: 3622
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L002_R2_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L002_R2_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L002_R2_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L002_R2_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L002_R2_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L002_R2_001.fastq.gz
    jobid: 3638
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L002_R2_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L002_R2_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L002_R2_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L002_R2_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L001_R2_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L001_R2_001.fastq.gz
    jobid: 3621
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L001_R2_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L001_R2_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L001_R2_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L001_R2_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L004_R1_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L004_R1_001.fastq.gz
    jobid: 3620
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L004_R1_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L004_R1_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L004_R1_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L004_R1_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L004_R2_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L004_R2_001.fastq.gz
    jobid: 3632
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L004_R2_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L004_R2_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L004_R2_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L004_R2_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD4_TH91_H3K4me3_S010R5H1.bed
    output: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD4_TH91_H3K4me3_S010R5H1.bed
    jobid: 2358
    reason: Missing output files: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD4_TH91_H3K4me3_S010R5H1.bed
    wildcards: filler=mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD4_TH91_H3K4me3_S010R5H1.bed

ln -srf '../mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD4_TH91_H3K4me3_S010R5H1.bed' 'out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD4_TH91_H3K4me3_S010R5H1.bed'

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: /gpfs/projects/spicuglia/mw/inp/fastq/202010026_R335_SS/fastq/Run_336_B/S003887_15_H3K4me3_LOUCY_DMSO_24H_1.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3_1.fastq.gz
    jobid: 3464
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3_1.fastq.gz
    wildcards: id=sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3_1.fastq.gz
    priority: 10

ln -srf '/gpfs/projects/spicuglia/mw/inp/fastq/202010026_R335_SS/fastq/Run_336_B/S003887_15_H3K4me3_LOUCY_DMSO_24H_1.fastq.gz' out/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3_1.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L004_R2_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L004_R2_001.fastq.gz
    jobid: 3640
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L004_R2_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L004_R2_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L004_R2_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L004_R2_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/blueprint/ChIP-Seq/ERS663693/ERR770351/ERR770351.fastq.gz
    output: out/ln/updir/mw/inp/fastq/blueprint/ChIP-Seq/ERS663693/ERR770351/ERR770351.fastq.gz
    jobid: 3685
    reason: Missing output files: out/ln/updir/mw/inp/fastq/blueprint/ChIP-Seq/ERS663693/ERR770351/ERR770351.fastq.gz
    wildcards: filler=mw/inp/fastq/blueprint/ChIP-Seq/ERS663693/ERR770351/ERR770351.fastq.gz

ln -srf '../mw/inp/fastq/blueprint/ChIP-Seq/ERS663693/ERR770351/ERR770351.fastq.gz' 'out/ln/updir/mw/inp/fastq/blueprint/ChIP-Seq/ERS663693/ERR770351/ERR770351.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: /gpfs/projects/spicuglia/mw/inp/fastq/run332/S003882_ChIP_PM_2.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3_2.fastq.gz
    jobid: 3455
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3_2.fastq.gz
    wildcards: id=sst/all_samples/fastq/Jurkat_PM_H3K4me3_2.fastq.gz
    priority: 10

ln -srf '/gpfs/projects/spicuglia/mw/inp/fastq/run332/S003882_ChIP_PM_2.fastq.gz' out/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3_2.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: /gpfs/projects/spicuglia/mw/inp/fastq/run332/S003880_ChIP_DMSO_1.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3_1.fastq.gz
    jobid: 3448
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3_1.fastq.gz
    wildcards: id=sst/all_samples/fastq/Jurkat_DMSO_H3K4me3_1.fastq.gz
    priority: 10

ln -srf '/gpfs/projects/spicuglia/mw/inp/fastq/run332/S003880_ChIP_DMSO_1.fastq.gz' out/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3_1.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L004_R2_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L004_R2_001.fastq.gz
    jobid: 3624
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L004_R2_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L004_R2_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L004_R2_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L004_R2_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: /gpfs/projects/spicuglia/mw/inp/fastq/run332/S003881_ChIP_OCIR_1.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3_1.fastq.gz
    jobid: 3452
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3_1.fastq.gz
    wildcards: id=sst/all_samples/fastq/Jurkat_OCIR_H3K4me3_1.fastq.gz
    priority: 10

ln -srf '/gpfs/projects/spicuglia/mw/inp/fastq/run332/S003881_ChIP_OCIR_1.fastq.gz' out/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3_1.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L001_R1_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L001_R1_001.fastq.gz
    jobid: 3609
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L001_R1_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L001_R1_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L001_R1_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L001_R1_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L003_R1_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L003_R1_001.fastq.gz
    jobid: 3635
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L003_R1_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L003_R1_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L003_R1_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L003_R1_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: /gpfs/projects/spicuglia/mw/inp/fastq/202010026_R335_SS/fastq/Run_336_B/S003888_16_H3K4me3_LOUCY_PBIT_5H_1.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3_1.fastq.gz
    jobid: 3466
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3_1.fastq.gz
    wildcards: id=sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3_1.fastq.gz
    priority: 10

ln -srf '/gpfs/projects/spicuglia/mw/inp/fastq/202010026_R335_SS/fastq/Run_336_B/S003888_16_H3K4me3_LOUCY_PBIT_5H_1.fastq.gz' out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3_1.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L001_R2_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L001_R2_001.fastq.gz
    jobid: 3637
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L001_R2_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L001_R2_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L001_R2_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L001_R2_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: /gpfs/projects/spicuglia/mw/inp/fastq/run332/S003880_ChIP_DMSO_2.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3_2.fastq.gz
    jobid: 3449
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3_2.fastq.gz
    wildcards: id=sst/all_samples/fastq/Jurkat_DMSO_H3K4me3_2.fastq.gz
    priority: 10

ln -srf '/gpfs/projects/spicuglia/mw/inp/fastq/run332/S003880_ChIP_DMSO_2.fastq.gz' out/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3_2.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L003_R2_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L003_R2_001.fastq.gz
    jobid: 3615
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L003_R2_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L003_R2_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L003_R2_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L003_R2_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: /gpfs/projects/spicuglia/mw/inp/fastq/run332/S003882_ChIP_PM_1.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3_1.fastq.gz
    jobid: 3454
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3_1.fastq.gz
    wildcards: id=sst/all_samples/fastq/Jurkat_PM_H3K4me3_1.fastq.gz
    priority: 10

ln -srf '/gpfs/projects/spicuglia/mw/inp/fastq/run332/S003882_ChIP_PM_1.fastq.gz' out/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3_1.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L004_R1_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L004_R1_001.fastq.gz
    jobid: 3612
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L004_R1_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L004_R1_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L004_R1_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L004_R1_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L002_R1_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L002_R1_001.fastq.gz
    jobid: 3626
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L002_R1_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L002_R1_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L002_R1_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L002_R1_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_Jurkat.bed
    output: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_Jurkat.bed
    jobid: 2206
    reason: Missing output files: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_Jurkat.bed
    wildcards: filler=mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_Jurkat.bed

ln -srf '../mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_Jurkat.bed' 'out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_Jurkat.bed'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L001_R1_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L001_R1_001.fastq.gz
    jobid: 3633
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L001_R1_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L001_R1_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L001_R1_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L001_R1_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/blueprint/ChIP-Seq/ERS663695/ERR770350/ERR770350.fastq.gz
    output: out/ln/updir/mw/inp/fastq/blueprint/ChIP-Seq/ERS663695/ERR770350/ERR770350.fastq.gz
    jobid: 3686
    reason: Missing output files: out/ln/updir/mw/inp/fastq/blueprint/ChIP-Seq/ERS663695/ERR770350/ERR770350.fastq.gz
    wildcards: filler=mw/inp/fastq/blueprint/ChIP-Seq/ERS663695/ERR770350/ERR770350.fastq.gz

ln -srf '../mw/inp/fastq/blueprint/ChIP-Seq/ERS663695/ERR770350/ERR770350.fastq.gz' 'out/ln/updir/mw/inp/fastq/blueprint/ChIP-Seq/ERS663695/ERR770350/ERR770350.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L002_R1_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L002_R1_001.fastq.gz
    jobid: 3610
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L002_R1_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L002_R1_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L002_R1_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L002_R1_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: /gpfs/projects/spicuglia/mw/inp/fastq/202010026_R335_SS/fastq/Run_336_B/S003886_14_H3K4me3_JURKAT_PBIT_24H_2.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3_2.fastq.gz
    jobid: 3463
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3_2.fastq.gz
    wildcards: id=sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3_2.fastq.gz
    priority: 10

ln -srf '/gpfs/projects/spicuglia/mw/inp/fastq/202010026_R335_SS/fastq/Run_336_B/S003886_14_H3K4me3_JURKAT_PBIT_24H_2.fastq.gz' out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3_2.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: /gpfs/projects/spicuglia/mw/inp/fastq/run332/S003881_ChIP_OCIR_2.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3_2.fastq.gz
    jobid: 3453
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3_2.fastq.gz
    wildcards: id=sst/all_samples/fastq/Jurkat_OCIR_H3K4me3_2.fastq.gz
    priority: 10

ln -srf '/gpfs/projects/spicuglia/mw/inp/fastq/run332/S003881_ChIP_OCIR_2.fastq.gz' out/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3_2.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L004_R2_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L004_R2_001.fastq.gz
    jobid: 3582
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L004_R2_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L004_R2_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L004_R2_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L004_R2_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: /gpfs/projects/spicuglia/mw/inp/fastq/run332/S003883_ChIP_RY_1.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3_1.fastq.gz
    jobid: 3456
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3_1.fastq.gz
    wildcards: id=sst/all_samples/fastq/Jurkat_RY_H3K4me3_1.fastq.gz
    priority: 10

ln -srf '/gpfs/projects/spicuglia/mw/inp/fastq/run332/S003883_ChIP_RY_1.fastq.gz' out/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3_1.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: /gpfs/projects/spicuglia/mw/inp/fastq/run332/S003883_ChIP_RY_2.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3_2.fastq.gz
    jobid: 3457
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3_2.fastq.gz
    wildcards: id=sst/all_samples/fastq/Jurkat_RY_H3K4me3_2.fastq.gz
    priority: 10

ln -srf '/gpfs/projects/spicuglia/mw/inp/fastq/run332/S003883_ChIP_RY_2.fastq.gz' out/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3_2.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L001_R2_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L001_R2_001.fastq.gz
    jobid: 3579
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L001_R2_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L001_R2_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L001_R2_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L001_R2_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L001_R1_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L001_R1_001.fastq.gz
    jobid: 3625
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L001_R1_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L001_R1_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L001_R1_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L001_R1_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L003_R2_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L003_R2_001.fastq.gz
    jobid: 3639
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L003_R2_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L003_R2_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L003_R2_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L003_R2_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run204/S002104_Loucy_PBIT_24h_10uM-72078/Loucy-PBIT-24h-10uM_S7_L001_R1_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run204/S002104_Loucy_PBIT_24h_10uM-72078/Loucy-PBIT-24h-10uM_S7_L001_R1_001.fastq.gz
    jobid: 3641
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run204/S002104_Loucy_PBIT_24h_10uM-72078/Loucy-PBIT-24h-10uM_S7_L001_R1_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run204/S002104_Loucy_PBIT_24h_10uM-72078/Loucy-PBIT-24h-10uM_S7_L001_R1_001.fastq.gz

ln -srf '../mw/inp/fastq/run204/S002104_Loucy_PBIT_24h_10uM-72078/Loucy-PBIT-24h-10uM_S7_L001_R1_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run204/S002104_Loucy_PBIT_24h_10uM-72078/Loucy-PBIT-24h-10uM_S7_L001_R1_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/blueprint/ChIP-Seq/ERS663694/ERR770349/ERR770349.fastq.gz
    output: out/ln/updir/mw/inp/fastq/blueprint/ChIP-Seq/ERS663694/ERR770349/ERR770349.fastq.gz
    jobid: 3687
    reason: Missing output files: out/ln/updir/mw/inp/fastq/blueprint/ChIP-Seq/ERS663694/ERR770349/ERR770349.fastq.gz
    wildcards: filler=mw/inp/fastq/blueprint/ChIP-Seq/ERS663694/ERR770349/ERR770349.fastq.gz

ln -srf '../mw/inp/fastq/blueprint/ChIP-Seq/ERS663694/ERR770349/ERR770349.fastq.gz' 'out/ln/updir/mw/inp/fastq/blueprint/ChIP-Seq/ERS663694/ERR770349/ERR770349.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L003_R1_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L003_R1_001.fastq.gz
    jobid: 3619
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L003_R1_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L003_R1_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L003_R1_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L003_R1_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L002_R2_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L002_R2_001.fastq.gz
    jobid: 3580
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L002_R2_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L002_R2_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L002_R2_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L002_R2_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: /gpfs/projects/spicuglia/mw/inp/fastq/202010026_R335_SS/fastq/Run_336_B/S003885_13_H3K4me3_JURKAT_PBIT_5H_2.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3_2.fastq.gz
    jobid: 3461
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3_2.fastq.gz
    wildcards: id=sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3_2.fastq.gz
    priority: 10

ln -srf '/gpfs/projects/spicuglia/mw/inp/fastq/202010026_R335_SS/fastq/Run_336_B/S003885_13_H3K4me3_JURKAT_PBIT_5H_2.fastq.gz' out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3_2.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L002_R1_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L002_R1_001.fastq.gz
    jobid: 3576
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L002_R1_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L002_R1_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L002_R1_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L002_R1_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L002_R1_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L002_R1_001.fastq.gz
    jobid: 3634
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L002_R1_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L002_R1_001.fastq.gz

ln -srf '../mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L002_R1_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L002_R1_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
localrule ln_srf_parent_dir:
    input: ../mw/inp/fastq/run204/S002104_Loucy_PBIT_24h_10uM-72078/Loucy-PBIT-24h-10uM_S7_L004_R1_001.fastq.gz
    output: out/ln/updir/mw/inp/fastq/run204/S002104_Loucy_PBIT_24h_10uM-72078/Loucy-PBIT-24h-10uM_S7_L004_R1_001.fastq.gz
    jobid: 3644
    reason: Missing output files: out/ln/updir/mw/inp/fastq/run204/S002104_Loucy_PBIT_24h_10uM-72078/Loucy-PBIT-24h-10uM_S7_L004_R1_001.fastq.gz
    wildcards: filler=mw/inp/fastq/run204/S002104_Loucy_PBIT_24h_10uM-72078/Loucy-PBIT-24h-10uM_S7_L004_R1_001.fastq.gz

ln -srf '../mw/inp/fastq/run204/S002104_Loucy_PBIT_24h_10uM-72078/Loucy-PBIT-24h-10uM_S7_L004_R1_001.fastq.gz' 'out/ln/updir/mw/inp/fastq/run204/S002104_Loucy_PBIT_24h_10uM-72078/Loucy-PBIT-24h-10uM_S7_L004_R1_001.fastq.gz'

[Sat Apr 17 13:59:03 2021]
rule wget_protocol:
    output: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.Y.fa.gz
    log: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.Y.fa.gz.log
    jobid: 3606
    benchmark: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.Y.fa.gz.benchmark.tsv
    reason: Missing output files: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.Y.fa.gz
    wildcards: protocol=ftp, path=ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.Y.fa.gz

wget --output-file=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.Y.fa.gz.log --output-document=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.Y.fa.gz ftp://ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.Y.fa.gz

[Sat Apr 17 13:59:03 2021]
rule sra_tools_fastq_dump_se_extra:
    output: out/sra-tools/fastq-dump_se/SRR568235.fastq.gz
    log: out/sra-tools/fastq-dump_se/SRR568235.fastq.gz.log
    jobid: 3720
    benchmark: out/sra-tools/fastq-dump_se/SRR568235.fastq.gz.benchmark.tsv
    reason: Missing output files: out/sra-tools/fastq-dump_se/SRR568235.fastq.gz
    wildcards: tool=sra-tools/fastq-dump_se, extra=, srr=SRR568235, ext=fastq.gz

fastq-dump  --gzip --outdir `dirname out/sra-tools/fastq-dump_se/SRR568235.fastq.gz` SRR568235 &> out/sra-tools/fastq-dump_se/SRR568235.fastq.gz.log

[Sat Apr 17 13:59:03 2021]
rule igvtools_tdftobedgraph:
    input: out/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.tdf
    output: out/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.BedGraph
    jobid: 3380
    reason: Missing output files: out/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.BedGraph
    wildcards: filler=wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph

igvtools tdftobedgraph out/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.tdf out/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.BedGraph

[Sat Apr 17 13:59:03 2021]
rule sra_tools_fastq_dump_se_extra:
    output: out/sra-tools/fastq-dump_se/SRR1536543.fastq.gz
    log: out/sra-tools/fastq-dump_se/SRR1536543.fastq.gz.log
    jobid: 3702
    benchmark: out/sra-tools/fastq-dump_se/SRR1536543.fastq.gz.benchmark.tsv
    reason: Missing output files: out/sra-tools/fastq-dump_se/SRR1536543.fastq.gz
    wildcards: tool=sra-tools/fastq-dump_se, extra=, srr=SRR1536543, ext=fastq.gz

fastq-dump  --gzip --outdir `dirname out/sra-tools/fastq-dump_se/SRR1536543.fastq.gz` SRR1536543 &> out/sra-tools/fastq-dump_se/SRR1536543.fastq.gz.log

[Sat Apr 17 13:59:03 2021]
rule wget_protocol:
    output: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.16.fa.gz
    log: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.16.fa.gz.log
    jobid: 3598
    benchmark: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.16.fa.gz.benchmark.tsv
    reason: Missing output files: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.16.fa.gz
    wildcards: protocol=ftp, path=ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.16.fa.gz

wget --output-file=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.16.fa.gz.log --output-document=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.16.fa.gz ftp://ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.16.fa.gz

[Sat Apr 17 13:59:03 2021]
rule wget_protocol:
    output: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.20.fa.gz
    log: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.20.fa.gz.log
    jobid: 3602
    benchmark: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.20.fa.gz.benchmark.tsv
    reason: Missing output files: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.20.fa.gz
    wildcards: protocol=ftp, path=ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.20.fa.gz

wget --output-file=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.20.fa.gz.log --output-document=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.20.fa.gz ftp://ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.20.fa.gz

[Sat Apr 17 13:59:03 2021]
rule wget_protocol:
    output: out/wget/https/ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.gtf.gz
    log: out/wget/https/ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.gtf.gz.log
    jobid: 3444
    benchmark: out/wget/https/ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.gtf.gz.benchmark.tsv
    reason: Missing output files: out/wget/https/ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.gtf.gz
    wildcards: protocol=https, path=ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.gtf.gz

wget --output-file=out/wget/https/ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.gtf.gz.log --output-document=out/wget/https/ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.gtf.gz https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.gtf.gz

[Sat Apr 17 13:59:03 2021]
rule wget_protocol:
    output: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.12.fa.gz
    log: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.12.fa.gz.log
    jobid: 3594
    benchmark: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.12.fa.gz.benchmark.tsv
    reason: Missing output files: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.12.fa.gz
    wildcards: protocol=ftp, path=ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.12.fa.gz

wget --output-file=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.12.fa.gz.log --output-document=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.12.fa.gz ftp://ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.12.fa.gz

[Sat Apr 17 13:59:03 2021]
rule igvtools_tdftobedgraph:
    input: out/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.tdf
    output: out/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.BedGraph
    jobid: 3377
    reason: Missing output files: out/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.BedGraph
    wildcards: filler=wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph

igvtools tdftobedgraph out/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.tdf out/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.BedGraph

[Sat Apr 17 13:59:03 2021]
rule sra_tools_fastq_dump_se_extra:
    output: out/sra-tools/fastq-dump_se/SRR11783980.fastq.gz
    log: out/sra-tools/fastq-dump_se/SRR11783980.fastq.gz.log
    jobid: 3707
    benchmark: out/sra-tools/fastq-dump_se/SRR11783980.fastq.gz.benchmark.tsv
    reason: Missing output files: out/sra-tools/fastq-dump_se/SRR11783980.fastq.gz
    wildcards: tool=sra-tools/fastq-dump_se, extra=, srr=SRR11783980, ext=fastq.gz

fastq-dump  --gzip --outdir `dirname out/sra-tools/fastq-dump_se/SRR11783980.fastq.gz` SRR11783980 &> out/sra-tools/fastq-dump_se/SRR11783980.fastq.gz.log

[Sat Apr 17 13:59:03 2021]
rule wget_protocol:
    output: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.8.fa.gz
    log: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.8.fa.gz.log
    jobid: 3590
    benchmark: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.8.fa.gz.benchmark.tsv
    reason: Missing output files: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.8.fa.gz
    wildcards: protocol=ftp, path=ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.8.fa.gz

wget --output-file=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.8.fa.gz.log --output-document=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.8.fa.gz ftp://ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.8.fa.gz

[Sat Apr 17 13:59:03 2021]
rule sra_tools_fastq_dump_se_extra:
    output: out/sra-tools/fastq-dump_se/SRR1536561.fastq.gz
    log: out/sra-tools/fastq-dump_se/SRR1536561.fastq.gz.log
    jobid: 3708
    benchmark: out/sra-tools/fastq-dump_se/SRR1536561.fastq.gz.benchmark.tsv
    reason: Missing output files: out/sra-tools/fastq-dump_se/SRR1536561.fastq.gz
    wildcards: tool=sra-tools/fastq-dump_se, extra=, srr=SRR1536561, ext=fastq.gz

fastq-dump  --gzip --outdir `dirname out/sra-tools/fastq-dump_se/SRR1536561.fastq.gz` SRR1536561 &> out/sra-tools/fastq-dump_se/SRR1536561.fastq.gz.log

[Sat Apr 17 13:59:03 2021]
rule sra_tools_fastq_dump_se_extra:
    output: out/sra-tools/fastq-dump_se/SRR5339377.fastq.gz
    log: out/sra-tools/fastq-dump_se/SRR5339377.fastq.gz.log
    jobid: 3723
    benchmark: out/sra-tools/fastq-dump_se/SRR5339377.fastq.gz.benchmark.tsv
    reason: Missing output files: out/sra-tools/fastq-dump_se/SRR5339377.fastq.gz
    wildcards: tool=sra-tools/fastq-dump_se, extra=, srr=SRR5339377, ext=fastq.gz

fastq-dump  --gzip --outdir `dirname out/sra-tools/fastq-dump_se/SRR5339377.fastq.gz` SRR5339377 &> out/sra-tools/fastq-dump_se/SRR5339377.fastq.gz.log

[Sat Apr 17 13:59:03 2021]
rule wget_protocol:
    output: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.nonchromosomal.fa.gz
    log: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.nonchromosomal.fa.gz.log
    jobid: 3608
    benchmark: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.nonchromosomal.fa.gz.benchmark.tsv
    reason: Missing output files: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.nonchromosomal.fa.gz
    wildcards: protocol=ftp, path=ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.nonchromosomal.fa.gz

wget --output-file=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.nonchromosomal.fa.gz.log --output-document=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.nonchromosomal.fa.gz ftp://ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.nonchromosomal.fa.gz

[Sat Apr 17 13:59:03 2021]
rule sra_tools_fastq_dump_se_extra:
    output: out/sra-tools/fastq-dump_se/SRR1536572.fastq.gz
    log: out/sra-tools/fastq-dump_se/SRR1536572.fastq.gz.log
    jobid: 3705
    benchmark: out/sra-tools/fastq-dump_se/SRR1536572.fastq.gz.benchmark.tsv
    reason: Missing output files: out/sra-tools/fastq-dump_se/SRR1536572.fastq.gz
    wildcards: tool=sra-tools/fastq-dump_se, extra=, srr=SRR1536572, ext=fastq.gz

fastq-dump  --gzip --outdir `dirname out/sra-tools/fastq-dump_se/SRR1536572.fastq.gz` SRR1536572 &> out/sra-tools/fastq-dump_se/SRR1536572.fastq.gz.log

[Sat Apr 17 13:59:03 2021]
rule wget_protocol:
    output: out/wget/ftp/ftp.ensembl.org/pub/release-100/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.28.dna_sm.toplevel.fa.gz
    log: out/wget/ftp/ftp.ensembl.org/pub/release-100/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.28.dna_sm.toplevel.fa.gz.log
    jobid: 3510
    benchmark: out/wget/ftp/ftp.ensembl.org/pub/release-100/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.28.dna_sm.toplevel.fa.gz.benchmark.tsv
    reason: Missing output files: out/wget/ftp/ftp.ensembl.org/pub/release-100/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.28.dna_sm.toplevel.fa.gz
    wildcards: protocol=ftp, path=ftp.ensembl.org/pub/release-100/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.28.dna_sm.toplevel.fa.gz

wget --output-file=out/wget/ftp/ftp.ensembl.org/pub/release-100/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.28.dna_sm.toplevel.fa.gz.log --output-document=out/wget/ftp/ftp.ensembl.org/pub/release-100/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.28.dna_sm.toplevel.fa.gz ftp://ftp.ensembl.org/pub/release-100/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.28.dna_sm.toplevel.fa.gz

[Sat Apr 17 13:59:03 2021]
rule sra_tools_fastq_dump_se_extra:
    output: out/sra-tools/fastq-dump_se/SRR568223.fastq.gz
    log: out/sra-tools/fastq-dump_se/SRR568223.fastq.gz.log
    jobid: 3718
    benchmark: out/sra-tools/fastq-dump_se/SRR568223.fastq.gz.benchmark.tsv
    reason: Missing output files: out/sra-tools/fastq-dump_se/SRR568223.fastq.gz
    wildcards: tool=sra-tools/fastq-dump_se, extra=, srr=SRR568223, ext=fastq.gz

fastq-dump  --gzip --outdir `dirname out/sra-tools/fastq-dump_se/SRR568223.fastq.gz` SRR568223 &> out/sra-tools/fastq-dump_se/SRR568223.fastq.gz.log

[Sat Apr 17 13:59:03 2021]
rule wget_protocol:
    output: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.10.fa.gz
    log: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.10.fa.gz.log
    jobid: 3592
    benchmark: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.10.fa.gz.benchmark.tsv
    reason: Missing output files: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.10.fa.gz
    wildcards: protocol=ftp, path=ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.10.fa.gz

wget --output-file=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.10.fa.gz.log --output-document=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.10.fa.gz ftp://ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.10.fa.gz

[Sat Apr 17 13:59:03 2021]
rule wget_protocol:
    output: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.5.fa.gz
    log: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.5.fa.gz.log
    jobid: 3587
    benchmark: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.5.fa.gz.benchmark.tsv
    reason: Missing output files: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.5.fa.gz
    wildcards: protocol=ftp, path=ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.5.fa.gz

wget --output-file=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.5.fa.gz.log --output-document=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.5.fa.gz ftp://ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.5.fa.gz

[Sat Apr 17 13:59:03 2021]
rule sra_tools_fastq_dump_se_extra:
    output: out/sra-tools/fastq-dump_se/SRR1536556.fastq.gz
    log: out/sra-tools/fastq-dump_se/SRR1536556.fastq.gz.log
    jobid: 3704
    benchmark: out/sra-tools/fastq-dump_se/SRR1536556.fastq.gz.benchmark.tsv
    reason: Missing output files: out/sra-tools/fastq-dump_se/SRR1536556.fastq.gz
    wildcards: tool=sra-tools/fastq-dump_se, extra=, srr=SRR1536556, ext=fastq.gz

fastq-dump  --gzip --outdir `dirname out/sra-tools/fastq-dump_se/SRR1536556.fastq.gz` SRR1536556 &> out/sra-tools/fastq-dump_se/SRR1536556.fastq.gz.log

[Sat Apr 17 13:59:03 2021]
rule sra_tools_fastq_dump_se_extra:
    output: out/sra-tools/fastq-dump_se/SRR1536552.fastq.gz
    log: out/sra-tools/fastq-dump_se/SRR1536552.fastq.gz.log
    jobid: 3703
    benchmark: out/sra-tools/fastq-dump_se/SRR1536552.fastq.gz.benchmark.tsv
    reason: Missing output files: out/sra-tools/fastq-dump_se/SRR1536552.fastq.gz
    wildcards: tool=sra-tools/fastq-dump_se, extra=, srr=SRR1536552, ext=fastq.gz

fastq-dump  --gzip --outdir `dirname out/sra-tools/fastq-dump_se/SRR1536552.fastq.gz` SRR1536552 &> out/sra-tools/fastq-dump_se/SRR1536552.fastq.gz.log

[Sat Apr 17 13:59:03 2021]
rule wget_protocol:
    output: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.17.fa.gz
    log: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.17.fa.gz.log
    jobid: 3599
    benchmark: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.17.fa.gz.benchmark.tsv
    reason: Missing output files: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.17.fa.gz
    wildcards: protocol=ftp, path=ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.17.fa.gz

wget --output-file=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.17.fa.gz.log --output-document=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.17.fa.gz ftp://ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.17.fa.gz

[Sat Apr 17 13:59:03 2021]
rule sra_tools_fastq_dump_se_extra:
    output: out/sra-tools/fastq-dump_se/SRR1057275.fastq.gz
    log: out/sra-tools/fastq-dump_se/SRR1057275.fastq.gz.log
    jobid: 3706
    benchmark: out/sra-tools/fastq-dump_se/SRR1057275.fastq.gz.benchmark.tsv
    reason: Missing output files: out/sra-tools/fastq-dump_se/SRR1057275.fastq.gz
    wildcards: tool=sra-tools/fastq-dump_se, extra=, srr=SRR1057275, ext=fastq.gz

fastq-dump  --gzip --outdir `dirname out/sra-tools/fastq-dump_se/SRR1057275.fastq.gz` SRR1057275 &> out/sra-tools/fastq-dump_se/SRR1057275.fastq.gz.log

[Sat Apr 17 13:59:03 2021]
rule wget_protocol:
    output: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.4.fa.gz
    log: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.4.fa.gz.log
    jobid: 3586
    benchmark: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.4.fa.gz.benchmark.tsv
    reason: Missing output files: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.4.fa.gz
    wildcards: protocol=ftp, path=ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.4.fa.gz

wget --output-file=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.4.fa.gz.log --output-document=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.4.fa.gz ftp://ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.4.fa.gz

[Sat Apr 17 13:59:03 2021]
rule wget_protocol:
    output: out/wget/ftp/ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz
    log: out/wget/ftp/ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz.log
    jobid: 3360
    benchmark: out/wget/ftp/ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz.benchmark.tsv
    reason: Missing output files: out/wget/ftp/ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz
    wildcards: protocol=ftp, path=ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz

wget --output-file=out/wget/ftp/ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz.log --output-document=out/wget/ftp/ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz ftp://ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz

[Sat Apr 17 13:59:03 2021]
rule wget_protocol:
    output: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.11.fa.gz
    log: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.11.fa.gz.log
    jobid: 3593
    benchmark: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.11.fa.gz.benchmark.tsv
    reason: Missing output files: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.11.fa.gz
    wildcards: protocol=ftp, path=ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.11.fa.gz

wget --output-file=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.11.fa.gz.log --output-document=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.11.fa.gz ftp://ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.11.fa.gz

[Sat Apr 17 13:59:03 2021]
rule wget_protocol:
    output: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.14.fa.gz
    log: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.14.fa.gz.log
    jobid: 3596
    benchmark: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.14.fa.gz.benchmark.tsv
    reason: Missing output files: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.14.fa.gz
    wildcards: protocol=ftp, path=ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.14.fa.gz

wget --output-file=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.14.fa.gz.log --output-document=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.14.fa.gz ftp://ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.14.fa.gz

[Sat Apr 17 13:59:03 2021]
rule sra_tools_fastq_dump_se_extra:
    output: out/sra-tools/fastq-dump_se/SRR568236.fastq.gz
    log: out/sra-tools/fastq-dump_se/SRR568236.fastq.gz.log
    jobid: 3721
    benchmark: out/sra-tools/fastq-dump_se/SRR568236.fastq.gz.benchmark.tsv
    reason: Missing output files: out/sra-tools/fastq-dump_se/SRR568236.fastq.gz
    wildcards: tool=sra-tools/fastq-dump_se, extra=, srr=SRR568236, ext=fastq.gz

fastq-dump  --gzip --outdir `dirname out/sra-tools/fastq-dump_se/SRR568236.fastq.gz` SRR568236 &> out/sra-tools/fastq-dump_se/SRR568236.fastq.gz.log

[Sat Apr 17 13:59:03 2021]
rule wget_protocol:
    output: out/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt.gz
    log: out/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt.gz.log
    jobid: 2208
    benchmark: out/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt.gz.benchmark.tsv
    reason: Missing output files: out/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt.gz
    wildcards: protocol=http, path=hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt.gz

wget --output-file=out/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt.gz.log --output-document=out/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt.gz http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt.gz

[Sat Apr 17 13:59:03 2021]
rule igvtools_tdftobedgraph:
    input: out/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.tdf
    output: out/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.BedGraph
    jobid: 3378
    reason: Missing output files: out/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.BedGraph
    wildcards: filler=wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph

igvtools tdftobedgraph out/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.tdf out/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.BedGraph

[Sat Apr 17 13:59:03 2021]
rule sra_tools_fastq_dump_se_extra:
    output: out/sra-tools/fastq-dump_se/SRR568224.fastq.gz
    log: out/sra-tools/fastq-dump_se/SRR568224.fastq.gz.log
    jobid: 3719
    benchmark: out/sra-tools/fastq-dump_se/SRR568224.fastq.gz.benchmark.tsv
    reason: Missing output files: out/sra-tools/fastq-dump_se/SRR568224.fastq.gz
    wildcards: tool=sra-tools/fastq-dump_se, extra=, srr=SRR568224, ext=fastq.gz

fastq-dump  --gzip --outdir `dirname out/sra-tools/fastq-dump_se/SRR568224.fastq.gz` SRR568224 &> out/sra-tools/fastq-dump_se/SRR568224.fastq.gz.log

[Sat Apr 17 13:59:03 2021]
rule sra_tools_fastq_dump_se_extra:
    output: out/sra-tools/fastq-dump_se/SRR5339376.fastq.gz
    log: out/sra-tools/fastq-dump_se/SRR5339376.fastq.gz.log
    jobid: 3722
    benchmark: out/sra-tools/fastq-dump_se/SRR5339376.fastq.gz.benchmark.tsv
    reason: Missing output files: out/sra-tools/fastq-dump_se/SRR5339376.fastq.gz
    wildcards: tool=sra-tools/fastq-dump_se, extra=, srr=SRR5339376, ext=fastq.gz

fastq-dump  --gzip --outdir `dirname out/sra-tools/fastq-dump_se/SRR5339376.fastq.gz` SRR5339376 &> out/sra-tools/fastq-dump_se/SRR5339376.fastq.gz.log

[Sat Apr 17 13:59:03 2021]
rule wget_protocol:
    output: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.1.fa.gz
    log: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.1.fa.gz.log
    jobid: 3583
    benchmark: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.1.fa.gz.benchmark.tsv
    reason: Missing output files: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.1.fa.gz
    wildcards: protocol=ftp, path=ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.1.fa.gz

wget --output-file=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.1.fa.gz.log --output-document=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.1.fa.gz ftp://ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.1.fa.gz

[Sat Apr 17 13:59:03 2021]
rule sra_tools_fastq_dump_se_extra:
    output: out/sra-tools/fastq-dump_se/SRR231122.fastq.gz
    log: out/sra-tools/fastq-dump_se/SRR231122.fastq.gz.log
    jobid: 3709
    benchmark: out/sra-tools/fastq-dump_se/SRR231122.fastq.gz.benchmark.tsv
    reason: Missing output files: out/sra-tools/fastq-dump_se/SRR231122.fastq.gz
    wildcards: tool=sra-tools/fastq-dump_se, extra=, srr=SRR231122, ext=fastq.gz

fastq-dump  --gzip --outdir `dirname out/sra-tools/fastq-dump_se/SRR231122.fastq.gz` SRR231122 &> out/sra-tools/fastq-dump_se/SRR231122.fastq.gz.log

[Sat Apr 17 13:59:03 2021]
rule sra_tools_fastq_dump_se_extra:
    output: out/sra-tools/fastq-dump_se/SRR2157609.fastq.gz
    log: out/sra-tools/fastq-dump_se/SRR2157609.fastq.gz.log
    jobid: 3668
    benchmark: out/sra-tools/fastq-dump_se/SRR2157609.fastq.gz.benchmark.tsv
    reason: Missing output files: out/sra-tools/fastq-dump_se/SRR2157609.fastq.gz
    wildcards: tool=sra-tools/fastq-dump_se, extra=, srr=SRR2157609, ext=fastq.gz

fastq-dump  --gzip --outdir `dirname out/sra-tools/fastq-dump_se/SRR2157609.fastq.gz` SRR2157609 &> out/sra-tools/fastq-dump_se/SRR2157609.fastq.gz.log

[Sat Apr 17 13:59:03 2021]
rule wget_protocol:
    output: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.3.fa.gz
    log: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.3.fa.gz.log
    jobid: 3585
    benchmark: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.3.fa.gz.benchmark.tsv
    reason: Missing output files: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.3.fa.gz
    wildcards: protocol=ftp, path=ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.3.fa.gz

wget --output-file=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.3.fa.gz.log --output-document=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.3.fa.gz ftp://ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.3.fa.gz

[Sat Apr 17 13:59:03 2021]
rule wget_protocol:
    output: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.6.fa.gz
    log: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.6.fa.gz.log
    jobid: 3588
    benchmark: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.6.fa.gz.benchmark.tsv
    reason: Missing output files: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.6.fa.gz
    wildcards: protocol=ftp, path=ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.6.fa.gz

wget --output-file=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.6.fa.gz.log --output-document=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.6.fa.gz ftp://ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.6.fa.gz

[Sat Apr 17 13:59:03 2021]
rule igvtools_tdftobedgraph:
    input: out/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.tdf
    output: out/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.BedGraph
    jobid: 3379
    reason: Missing output files: out/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.BedGraph
    wildcards: filler=wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph

igvtools tdftobedgraph out/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.tdf out/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.BedGraph

[Sat Apr 17 13:59:03 2021]
rule wget_protocol:
    output: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.15.fa.gz
    log: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.15.fa.gz.log
    jobid: 3597
    benchmark: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.15.fa.gz.benchmark.tsv
    reason: Missing output files: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.15.fa.gz
    wildcards: protocol=ftp, path=ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.15.fa.gz

wget --output-file=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.15.fa.gz.log --output-document=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.15.fa.gz ftp://ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.15.fa.gz

[Sat Apr 17 13:59:03 2021]
rule wget_protocol:
    output: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.13.fa.gz
    log: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.13.fa.gz.log
    jobid: 3595
    benchmark: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.13.fa.gz.benchmark.tsv
    reason: Missing output files: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.13.fa.gz
    wildcards: protocol=ftp, path=ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.13.fa.gz

wget --output-file=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.13.fa.gz.log --output-document=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.13.fa.gz ftp://ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.13.fa.gz

[Sat Apr 17 13:59:03 2021]
rule wget_protocol:
    output: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.18.fa.gz
    log: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.18.fa.gz.log
    jobid: 3600
    benchmark: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.18.fa.gz.benchmark.tsv
    reason: Missing output files: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.18.fa.gz
    wildcards: protocol=ftp, path=ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.18.fa.gz

wget --output-file=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.18.fa.gz.log --output-document=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.18.fa.gz ftp://ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.18.fa.gz

[Sat Apr 17 13:59:03 2021]
rule wget_protocol:
    output: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.7.fa.gz
    log: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.7.fa.gz.log
    jobid: 3589
    benchmark: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.7.fa.gz.benchmark.tsv
    reason: Missing output files: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.7.fa.gz
    wildcards: protocol=ftp, path=ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.7.fa.gz

wget --output-file=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.7.fa.gz.log --output-document=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.7.fa.gz ftp://ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.7.fa.gz

[Sat Apr 17 13:59:03 2021]
rule wget_protocol:
    output: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.9.fa.gz
    log: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.9.fa.gz.log
    jobid: 3591
    benchmark: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.9.fa.gz.benchmark.tsv
    reason: Missing output files: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.9.fa.gz
    wildcards: protocol=ftp, path=ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.9.fa.gz

wget --output-file=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.9.fa.gz.log --output-document=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.9.fa.gz ftp://ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.9.fa.gz

[Sat Apr 17 13:59:03 2021]
rule wget_protocol:
    output: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.X.fa.gz
    log: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.X.fa.gz.log
    jobid: 3605
    benchmark: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.X.fa.gz.benchmark.tsv
    reason: Missing output files: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.X.fa.gz
    wildcards: protocol=ftp, path=ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.X.fa.gz

wget --output-file=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.X.fa.gz.log --output-document=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.X.fa.gz ftp://ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.X.fa.gz

[Sat Apr 17 13:59:03 2021]
rule wget_protocol:
    output: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.2.fa.gz
    log: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.2.fa.gz.log
    jobid: 3584
    benchmark: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.2.fa.gz.benchmark.tsv
    reason: Missing output files: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.2.fa.gz
    wildcards: protocol=ftp, path=ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.2.fa.gz

wget --output-file=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.2.fa.gz.log --output-document=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.2.fa.gz ftp://ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.2.fa.gz

[Sat Apr 17 13:59:03 2021]
rule wget_protocol:
    output: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.MT.fa.gz
    log: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.MT.fa.gz.log
    jobid: 3607
    benchmark: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.MT.fa.gz.benchmark.tsv
    reason: Missing output files: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.MT.fa.gz
    wildcards: protocol=ftp, path=ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.MT.fa.gz

wget --output-file=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.MT.fa.gz.log --output-document=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.MT.fa.gz ftp://ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.MT.fa.gz

[Sat Apr 17 13:59:03 2021]
rule wget_protocol:
    output: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.19.fa.gz
    log: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.19.fa.gz.log
    jobid: 3601
    benchmark: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.19.fa.gz.benchmark.tsv
    reason: Missing output files: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.19.fa.gz
    wildcards: protocol=ftp, path=ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.19.fa.gz

wget --output-file=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.19.fa.gz.log --output-document=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.19.fa.gz ftp://ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.19.fa.gz

[Sat Apr 17 13:59:03 2021]
rule wget_protocol:
    output: out/wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf.gz
    log: out/wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf.gz.log
    jobid: 3473
    benchmark: out/wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf.gz.benchmark.tsv
    reason: Missing output files: out/wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf.gz
    wildcards: protocol=ftp, path=ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf.gz

wget --output-file=out/wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf.gz.log --output-document=out/wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf.gz ftp://ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf.gz

[Sat Apr 17 13:59:03 2021]
rule sra_tools_fastq_dump_se_extra:
    output: out/sra-tools/fastq-dump_se/SRR5338727.fastq.gz
    log: out/sra-tools/fastq-dump_se/SRR5338727.fastq.gz.log
    jobid: 3710
    benchmark: out/sra-tools/fastq-dump_se/SRR5338727.fastq.gz.benchmark.tsv
    reason: Missing output files: out/sra-tools/fastq-dump_se/SRR5338727.fastq.gz
    wildcards: tool=sra-tools/fastq-dump_se, extra=, srr=SRR5338727, ext=fastq.gz

fastq-dump  --gzip --outdir `dirname out/sra-tools/fastq-dump_se/SRR5338727.fastq.gz` SRR5338727 &> out/sra-tools/fastq-dump_se/SRR5338727.fastq.gz.log

[Sat Apr 17 13:59:03 2021]
rule wget_protocol:
    output: out/wget/http/igenomes.illumina.com.s3-website-us-east-1.amazonaws.com/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz
    log: out/wget/http/igenomes.illumina.com.s3-website-us-east-1.amazonaws.com/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz.log
    jobid: 3450
    benchmark: out/wget/http/igenomes.illumina.com.s3-website-us-east-1.amazonaws.com/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz.benchmark.tsv
    reason: Missing output files: out/wget/http/igenomes.illumina.com.s3-website-us-east-1.amazonaws.com/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz
    wildcards: protocol=http, path=igenomes.illumina.com.s3-website-us-east-1.amazonaws.com/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz

wget --output-file=out/wget/http/igenomes.illumina.com.s3-website-us-east-1.amazonaws.com/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz.log --output-document=out/wget/http/igenomes.illumina.com.s3-website-us-east-1.amazonaws.com/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz http://igenomes.illumina.com.s3-website-us-east-1.amazonaws.com/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz

[Sat Apr 17 13:59:03 2021]
rule wget_protocol:
    output: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.22.fa.gz
    log: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.22.fa.gz.log
    jobid: 3604
    benchmark: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.22.fa.gz.benchmark.tsv
    reason: Missing output files: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.22.fa.gz
    wildcards: protocol=ftp, path=ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.22.fa.gz

wget --output-file=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.22.fa.gz.log --output-document=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.22.fa.gz ftp://ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.22.fa.gz

[Sat Apr 17 13:59:03 2021]
rule wget_protocol:
    output: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.21.fa.gz
    log: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.21.fa.gz.log
    jobid: 3603
    benchmark: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.21.fa.gz.benchmark.tsv
    reason: Missing output files: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.21.fa.gz
    wildcards: protocol=ftp, path=ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.21.fa.gz

wget --output-file=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.21.fa.gz.log --output-document=out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.21.fa.gz ftp://ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.21.fa.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: out/sra-tools/fastq-dump_se/SRR5339376.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Loucy_SRR5339376_H3K36me3.fastq.gz
    jobid: 3716
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Loucy_SRR5339376_H3K36me3.fastq.gz; Input files updated by another job: out/sra-tools/fastq-dump_se/SRR5339376.fastq.gz
    wildcards: id=sst/all_samples/fastq/Loucy_SRR5339376_H3K36me3.fastq.gz
    priority: 10

ln -srf 'out/sra-tools/fastq-dump_se/SRR5339376.fastq.gz' out/ln/alias/sst/all_samples/fastq/Loucy_SRR5339376_H3K36me3.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: out/ln/updir/mw/inp/fastq/blueprint/ChIP-Seq/ERS663693/ERR770351/ERR770351.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.fastq.gz
    jobid: 3669
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.fastq.gz; Input files updated by another job: out/ln/updir/mw/inp/fastq/blueprint/ChIP-Seq/ERS663693/ERR770351/ERR770351.fastq.gz
    wildcards: id=sst/all_samples/fastq/TH91_SP8_H3K4me3.fastq.gz
    priority: 10

ln -srf 'out/ln/updir/mw/inp/fastq/blueprint/ChIP-Seq/ERS663693/ERR770351/ERR770351.fastq.gz' out/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: out/sra-tools/fastq-dump_se/SRR568224.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/DND-41_SRR568224_H3K36me3.fastq.gz
    jobid: 3713
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/DND-41_SRR568224_H3K36me3.fastq.gz; Input files updated by another job: out/sra-tools/fastq-dump_se/SRR568224.fastq.gz
    wildcards: id=sst/all_samples/fastq/DND-41_SRR568224_H3K36me3.fastq.gz
    priority: 10

ln -srf 'out/sra-tools/fastq-dump_se/SRR568224.fastq.gz' out/ln/alias/sst/all_samples/fastq/DND-41_SRR568224_H3K36me3.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: out/sra-tools/fastq-dump_se/SRR568236.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/DND-41_SRR568236_H3K79me2.fastq.gz
    jobid: 3715
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/DND-41_SRR568236_H3K79me2.fastq.gz; Input files updated by another job: out/sra-tools/fastq-dump_se/SRR568236.fastq.gz
    wildcards: id=sst/all_samples/fastq/DND-41_SRR568236_H3K79me2.fastq.gz
    priority: 10

ln -srf 'out/sra-tools/fastq-dump_se/SRR568236.fastq.gz' out/ln/alias/sst/all_samples/fastq/DND-41_SRR568236_H3K79me2.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: out/ln/updir/mw/inp/fastq/blueprint/ChIP-Seq/ERS663695/ERR770350/ERR770350.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.fastq.gz
    jobid: 3670
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.fastq.gz; Input files updated by another job: out/ln/updir/mw/inp/fastq/blueprint/ChIP-Seq/ERS663695/ERR770350/ERR770350.fastq.gz
    wildcards: id=sst/all_samples/fastq/TH91_SP4_H3K4me3.fastq.gz
    priority: 10

ln -srf 'out/ln/updir/mw/inp/fastq/blueprint/ChIP-Seq/ERS663695/ERR770350/ERR770350.fastq.gz' out/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: out/sra-tools/fastq-dump_se/SRR568223.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/DND-41_SRR568223_H3K36me3.fastq.gz
    jobid: 3712
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/DND-41_SRR568223_H3K36me3.fastq.gz; Input files updated by another job: out/sra-tools/fastq-dump_se/SRR568223.fastq.gz
    wildcards: id=sst/all_samples/fastq/DND-41_SRR568223_H3K36me3.fastq.gz
    priority: 10

ln -srf 'out/sra-tools/fastq-dump_se/SRR568223.fastq.gz' out/ln/alias/sst/all_samples/fastq/DND-41_SRR568223_H3K36me3.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: out/sra-tools/fastq-dump_se/SRR231122.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.fastq.gz
    jobid: 3697
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.fastq.gz; Input files updated by another job: out/sra-tools/fastq-dump_se/SRR231122.fastq.gz
    wildcards: id=sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.fastq.gz
    priority: 10

ln -srf 'out/sra-tools/fastq-dump_se/SRR231122.fastq.gz' out/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: out/sra-tools/fastq-dump_se/SRR11783980.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.fastq.gz
    jobid: 3695
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.fastq.gz; Input files updated by another job: out/sra-tools/fastq-dump_se/SRR11783980.fastq.gz
    wildcards: id=sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.fastq.gz
    priority: 10

ln -srf 'out/sra-tools/fastq-dump_se/SRR11783980.fastq.gz' out/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: out/ln/updir/mw/inp/fastq/blueprint/ChIP-Seq/ERS663694/ERR770349/ERR770349.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.fastq.gz
    jobid: 3671
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.fastq.gz; Input files updated by another job: out/ln/updir/mw/inp/fastq/blueprint/ChIP-Seq/ERS663694/ERR770349/ERR770349.fastq.gz
    wildcards: id=sst/all_samples/fastq/TH91_LC_H3K4me3.fastq.gz
    priority: 10

ln -srf 'out/ln/updir/mw/inp/fastq/blueprint/ChIP-Seq/ERS663694/ERR770349/ERR770349.fastq.gz' out/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: out/sra-tools/fastq-dump_se/SRR1536543.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.fastq.gz
    jobid: 3690
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.fastq.gz; Input files updated by another job: out/sra-tools/fastq-dump_se/SRR1536543.fastq.gz
    wildcards: id=sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.fastq.gz
    priority: 10

ln -srf 'out/sra-tools/fastq-dump_se/SRR1536543.fastq.gz' out/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: out/sra-tools/fastq-dump_se/SRR568235.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/DND-41_SRR568235_H3K79me2.fastq.gz
    jobid: 3714
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/DND-41_SRR568235_H3K79me2.fastq.gz; Input files updated by another job: out/sra-tools/fastq-dump_se/SRR568235.fastq.gz
    wildcards: id=sst/all_samples/fastq/DND-41_SRR568235_H3K79me2.fastq.gz
    priority: 10

ln -srf 'out/sra-tools/fastq-dump_se/SRR568235.fastq.gz' out/ln/alias/sst/all_samples/fastq/DND-41_SRR568235_H3K79me2.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: out/sra-tools/fastq-dump_se/SRR1536556.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.fastq.gz
    jobid: 3692
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.fastq.gz; Input files updated by another job: out/sra-tools/fastq-dump_se/SRR1536556.fastq.gz
    wildcards: id=sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.fastq.gz
    priority: 10

ln -srf 'out/sra-tools/fastq-dump_se/SRR1536556.fastq.gz' out/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: out/sra-tools/fastq-dump_se/SRR1536561.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.fastq.gz
    jobid: 3696
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.fastq.gz; Input files updated by another job: out/sra-tools/fastq-dump_se/SRR1536561.fastq.gz
    wildcards: id=sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.fastq.gz
    priority: 10

ln -srf 'out/sra-tools/fastq-dump_se/SRR1536561.fastq.gz' out/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: out/sra-tools/fastq-dump_se/SRR1057275.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.fastq.gz
    jobid: 3694
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.fastq.gz; Input files updated by another job: out/sra-tools/fastq-dump_se/SRR1057275.fastq.gz
    wildcards: id=sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.fastq.gz
    priority: 10

ln -srf 'out/sra-tools/fastq-dump_se/SRR1057275.fastq.gz' out/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: out/sra-tools/fastq-dump_se/SRR5338727.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.fastq.gz
    jobid: 3698
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.fastq.gz; Input files updated by another job: out/sra-tools/fastq-dump_se/SRR5338727.fastq.gz
    wildcards: id=sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.fastq.gz
    priority: 10

ln -srf 'out/sra-tools/fastq-dump_se/SRR5338727.fastq.gz' out/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: out/sra-tools/fastq-dump_se/SRR2157609.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.fastq.gz
    jobid: 3571
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.fastq.gz; Input files updated by another job: out/sra-tools/fastq-dump_se/SRR2157609.fastq.gz
    wildcards: id=sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.fastq.gz
    priority: 10

ln -srf 'out/sra-tools/fastq-dump_se/SRR2157609.fastq.gz' out/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: out/sra-tools/fastq-dump_se/SRR5339377.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Loucy_SRR5339377_H3K36me3.fastq.gz
    jobid: 3717
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Loucy_SRR5339377_H3K36me3.fastq.gz; Input files updated by another job: out/sra-tools/fastq-dump_se/SRR5339377.fastq.gz
    wildcards: id=sst/all_samples/fastq/Loucy_SRR5339377_H3K36me3.fastq.gz
    priority: 10

ln -srf 'out/sra-tools/fastq-dump_se/SRR5339377.fastq.gz' out/ln/alias/sst/all_samples/fastq/Loucy_SRR5339377_H3K36me3.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: out/sra-tools/fastq-dump_se/SRR1536552.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.fastq.gz
    jobid: 3691
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.fastq.gz; Input files updated by another job: out/sra-tools/fastq-dump_se/SRR1536552.fastq.gz
    wildcards: id=sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.fastq.gz
    priority: 10

ln -srf 'out/sra-tools/fastq-dump_se/SRR1536552.fastq.gz' out/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: out/ln/updir/mw/inp/fastq/blueprint/ChIP-Seq/ERS663696/ERR770348/ERR770348.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.fastq.gz
    jobid: 3667
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.fastq.gz; Input files updated by another job: out/ln/updir/mw/inp/fastq/blueprint/ChIP-Seq/ERS663696/ERR770348/ERR770348.fastq.gz
    wildcards: id=sst/all_samples/fastq/TH91_EC_H3K4me3.fastq.gz
    priority: 10

ln -srf 'out/ln/updir/mw/inp/fastq/blueprint/ChIP-Seq/ERS663696/ERR770348/ERR770348.fastq.gz' out/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.fastq.gz

[Sat Apr 17 13:59:03 2021]
localrule ln_alias:
    input: out/sra-tools/fastq-dump_se/SRR1536572.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.fastq.gz
    jobid: 3693
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.fastq.gz; Input files updated by another job: out/sra-tools/fastq-dump_se/SRR1536572.fastq.gz
    wildcards: id=sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.fastq.gz
    priority: 10

ln -srf 'out/sra-tools/fastq-dump_se/SRR1536572.fastq.gz' out/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.fastq.gz

[Sat Apr 17 13:59:03 2021]
rule gunzip_extra:
    input: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.6.fa.gz
    output: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.6.fa
    log: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.6.fa.log
    jobid: 3518
    benchmark: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.6.fa.benchmark.tsv
    reason: Missing output files: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.6.fa; Input files updated by another job: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.6.fa.gz
    wildcards: tool=gunzip/, extra=to-stdout, filler=wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.6.fa

gunzip --to-stdout out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.6.fa.gz > out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.6.fa 2> out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.6.fa.log

[Sat Apr 17 13:59:03 2021]
rule sickle_pe_extra:
    input: out/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3_1.fastq.gz, out/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3_2.fastq.gz
    output: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3_2.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3_single.fastq.gz
    log: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.fastq.gz.log
    jobid: 3408
    reason: Missing output files: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3_2.fastq.gz; Input files updated by another job: out/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3_1.fastq.gz, out/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3_2.fastq.gz
    wildcards: tool=sickle/pe, extra=_-t_sanger_-q_20, filler=ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3, ext=fastq.gz

sickle pe -f out/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3_1.fastq.gz -r out/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3_2.fastq.gz -o out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3_1.fastq.gz -p out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3_2.fastq.gz -s out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3_single.fastq.gz  -t sanger -q 20 -g &> out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.fastq.gz.log

[Sat Apr 17 13:59:04 2021]
rule gunzip_extra:
    input: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.19.fa.gz
    output: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.19.fa
    log: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.19.fa.log
    jobid: 3531
    benchmark: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.19.fa.benchmark.tsv
    reason: Missing output files: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.19.fa; Input files updated by another job: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.19.fa.gz
    wildcards: tool=gunzip/, extra=to-stdout, filler=wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.19.fa

gunzip --to-stdout out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.19.fa.gz > out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.19.fa 2> out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.19.fa.log

[Sat Apr 17 13:59:04 2021]
rule sickle_pe_extra:
    input: out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3_1.fastq.gz, out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3_2.fastq.gz
    output: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3_2.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3_single.fastq.gz
    log: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.fastq.gz.log
    jobid: 3407
    reason: Missing output files: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3_2.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3_1.fastq.gz; Input files updated by another job: out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3_2.fastq.gz, out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3_1.fastq.gz
    wildcards: tool=sickle/pe, extra=_-t_sanger_-q_20, filler=ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3, ext=fastq.gz

sickle pe -f out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3_1.fastq.gz -r out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3_2.fastq.gz -o out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3_1.fastq.gz -p out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3_2.fastq.gz -s out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3_single.fastq.gz  -t sanger -q 20 -g &> out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.fastq.gz.log

[Sat Apr 17 13:59:04 2021]
rule sickle_pe_extra:
    input: out/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3_1.fastq.gz, out/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3_2.fastq.gz
    output: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3_2.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3_single.fastq.gz
    log: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.fastq.gz.log
    jobid: 3402
    reason: Missing output files: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3_2.fastq.gz; Input files updated by another job: out/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3_2.fastq.gz, out/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3_1.fastq.gz
    wildcards: tool=sickle/pe, extra=_-t_sanger_-q_20, filler=ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3, ext=fastq.gz

sickle pe -f out/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3_1.fastq.gz -r out/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3_2.fastq.gz -o out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3_1.fastq.gz -p out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3_2.fastq.gz -s out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3_single.fastq.gz  -t sanger -q 20 -g &> out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.fastq.gz.log

[Sat Apr 17 13:59:04 2021]
rule gunzip_extra:
    input: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.12.fa.gz
    output: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.12.fa
    log: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.12.fa.log
    jobid: 3524
    benchmark: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.12.fa.benchmark.tsv
    reason: Missing output files: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.12.fa; Input files updated by another job: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.12.fa.gz
    wildcards: tool=gunzip/, extra=to-stdout, filler=wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.12.fa

gunzip --to-stdout out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.12.fa.gz > out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.12.fa 2> out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.12.fa.log

[Sat Apr 17 13:59:04 2021]
rule gunzip_extra:
    input: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.5.fa.gz
    output: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.5.fa
    log: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.5.fa.log
    jobid: 3517
    benchmark: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.5.fa.benchmark.tsv
    reason: Missing output files: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.5.fa; Input files updated by another job: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.5.fa.gz
    wildcards: tool=gunzip/, extra=to-stdout, filler=wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.5.fa

gunzip --to-stdout out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.5.fa.gz > out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.5.fa 2> out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.5.fa.log

[Sat Apr 17 13:59:04 2021]
rule gunzip_extra:
    input: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.14.fa.gz
    output: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.14.fa
    log: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.14.fa.log
    jobid: 3526
    benchmark: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.14.fa.benchmark.tsv
    reason: Missing output files: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.14.fa; Input files updated by another job: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.14.fa.gz
    wildcards: tool=gunzip/, extra=to-stdout, filler=wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.14.fa

gunzip --to-stdout out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.14.fa.gz > out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.14.fa 2> out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.14.fa.log

[Sat Apr 17 13:59:04 2021]
rule sickle_pe_extra:
    input: out/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3_1.fastq.gz, out/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3_2.fastq.gz
    output: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3_2.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3_single.fastq.gz
    log: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.fastq.gz.log
    jobid: 3405
    reason: Missing output files: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3_2.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3_1.fastq.gz; Input files updated by another job: out/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3_1.fastq.gz, out/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3_2.fastq.gz
    wildcards: tool=sickle/pe, extra=_-t_sanger_-q_20, filler=ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3, ext=fastq.gz

sickle pe -f out/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3_1.fastq.gz -r out/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3_2.fastq.gz -o out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3_1.fastq.gz -p out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3_2.fastq.gz -s out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3_single.fastq.gz  -t sanger -q 20 -g &> out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.fastq.gz.log

[Sat Apr 17 13:59:04 2021]
rule sort_extra:
    input: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_Jurkat.bed
    output: out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_Jurkat.bed
    jobid: 35
    reason: Missing output files: out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_Jurkat.bed; Input files updated by another job: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_Jurkat.bed
    wildcards: tool=sort/, extra=_-u, filler=ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_Jurkat.bed

LC_ALL=C; sort  -u out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_Jurkat.bed > out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_Jurkat.bed

[Sat Apr 17 13:59:04 2021]
rule sort_extra:
    input: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_Jurkat.bed
    output: out/sort/_-u_-k1,1_-k2,2n/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_Jurkat.bed
    jobid: 32
    reason: Missing output files: out/sort/_-u_-k1,1_-k2,2n/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_Jurkat.bed; Input files updated by another job: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_Jurkat.bed
    wildcards: tool=sort/, extra=_-u_-k1,1_-k2,2n, filler=ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_Jurkat.bed

LC_ALL=C; sort  -u -k1,1 -k2,2n out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_Jurkat.bed > out/sort/_-u_-k1,1_-k2,2n/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_Jurkat.bed

[Sat Apr 17 13:59:04 2021]
rule sort_extra:
    input: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_Jurkat.bed
    output: out/sort/_-u_-k1,1_-k2,2n/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_Jurkat.bed
    jobid: 33
    reason: Missing output files: out/sort/_-u_-k1,1_-k2,2n/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_Jurkat.bed; Input files updated by another job: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_Jurkat.bed
    wildcards: tool=sort/, extra=_-u_-k1,1_-k2,2n, filler=ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_Jurkat.bed

LC_ALL=C; sort  -u -k1,1 -k2,2n out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_Jurkat.bed > out/sort/_-u_-k1,1_-k2,2n/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_Jurkat.bed

[Sat Apr 17 13:59:04 2021]
rule sort_extra:
    input: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_Jurkat.bed
    output: out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_Jurkat.bed
    jobid: 321
    reason: Missing output files: out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_Jurkat.bed; Input files updated by another job: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_Jurkat.bed
    wildcards: tool=sort/, extra=_-u, filler=ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_Jurkat.bed

LC_ALL=C; sort  -u out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_Jurkat.bed > out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_Jurkat.bed

[Sat Apr 17 13:59:04 2021]
rule cat:
    input: out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L001_R1_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L002_R1_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L003_R1_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L004_R1_001.fastq.gz
    output: out/cat/merge-nexsteq500-pe/Loucy_DMSO_5h_1.fastq.gz
    jobid: 3543
    reason: Missing output files: out/cat/merge-nexsteq500-pe/Loucy_DMSO_5h_1.fastq.gz; Input files updated by another job: out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L004_R1_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L001_R1_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L003_R1_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L002_R1_001.fastq.gz
    wildcards: cat_id=merge-nexsteq500-pe/Loucy_DMSO_5h_1.fastq.gz

cat out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L001_R1_001.fastq.gz out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L002_R1_001.fastq.gz out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L003_R1_001.fastq.gz out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L004_R1_001.fastq.gz > out/cat/merge-nexsteq500-pe/Loucy_DMSO_5h_1.fastq.gz

[Sat Apr 17 13:59:04 2021]
rule cat:
    input: out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L001_R1_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L002_R1_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L003_R1_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L004_R1_001.fastq.gz
    output: out/cat/merge-nexsteq500-pe/Jurkat_DMSO_5h_1.fastq.gz
    jobid: 3511
    reason: Missing output files: out/cat/merge-nexsteq500-pe/Jurkat_DMSO_5h_1.fastq.gz; Input files updated by another job: out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L002_R1_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L004_R1_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L003_R1_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L001_R1_001.fastq.gz
    wildcards: cat_id=merge-nexsteq500-pe/Jurkat_DMSO_5h_1.fastq.gz

cat out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L001_R1_001.fastq.gz out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L002_R1_001.fastq.gz out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L003_R1_001.fastq.gz out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L004_R1_001.fastq.gz > out/cat/merge-nexsteq500-pe/Jurkat_DMSO_5h_1.fastq.gz

[Sat Apr 17 13:59:04 2021]
rule sort_extra:
    input: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD8_TH91_H3K4me3_S010S3H1.bed
    output: out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD8_TH91_H3K4me3_S010S3H1.bed
    jobid: 333
    reason: Missing output files: out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD8_TH91_H3K4me3_S010S3H1.bed; Input files updated by another job: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD8_TH91_H3K4me3_S010S3H1.bed
    wildcards: tool=sort/, extra=_-u, filler=ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD8_TH91_H3K4me3_S010S3H1.bed

LC_ALL=C; sort  -u out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD8_TH91_H3K4me3_S010S3H1.bed > out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD8_TH91_H3K4me3_S010S3H1.bed

[Sat Apr 17 13:59:04 2021]
rule gunzip_extra:
    input: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.3.fa.gz
    output: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.3.fa
    log: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.3.fa.log
    jobid: 3515
    benchmark: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.3.fa.benchmark.tsv
    reason: Missing output files: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.3.fa; Input files updated by another job: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.3.fa.gz
    wildcards: tool=gunzip/, extra=to-stdout, filler=wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.3.fa

gunzip --to-stdout out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.3.fa.gz > out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.3.fa 2> out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.3.fa.log

[Sat Apr 17 13:59:04 2021]
rule cat:
    input: out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L001_R2_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L002_R2_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L003_R2_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L004_R2_001.fastq.gz
    output: out/cat/merge-nexsteq500-pe/Jurkat_DMSO_5h_2.fastq.gz
    jobid: 3512
    reason: Missing output files: out/cat/merge-nexsteq500-pe/Jurkat_DMSO_5h_2.fastq.gz; Input files updated by another job: out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L001_R2_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L004_R2_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L003_R2_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L002_R2_001.fastq.gz
    wildcards: cat_id=merge-nexsteq500-pe/Jurkat_DMSO_5h_2.fastq.gz

cat out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L001_R2_001.fastq.gz out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L002_R2_001.fastq.gz out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L003_R2_001.fastq.gz out/ln/updir/mw/inp/fastq/run189/S001833_Jurkat_PBIT_5h_DMSO-60062/Jurkat-PBIT-5h-DMSO_S3_L004_R2_001.fastq.gz > out/cat/merge-nexsteq500-pe/Jurkat_DMSO_5h_2.fastq.gz

[Sat Apr 17 13:59:04 2021]
rule cat:
    input: out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L001_R2_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L002_R2_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L003_R2_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L004_R2_001.fastq.gz
    output: out/cat/merge-nexsteq500-pe/Jurkat_PBIT_5h_10uM_2.fastq.gz
    jobid: 3540
    reason: Missing output files: out/cat/merge-nexsteq500-pe/Jurkat_PBIT_5h_10uM_2.fastq.gz; Input files updated by another job: out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L003_R2_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L001_R2_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L002_R2_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L004_R2_001.fastq.gz
    wildcards: cat_id=merge-nexsteq500-pe/Jurkat_PBIT_5h_10uM_2.fastq.gz

cat out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L001_R2_001.fastq.gz out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L002_R2_001.fastq.gz out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L003_R2_001.fastq.gz out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L004_R2_001.fastq.gz > out/cat/merge-nexsteq500-pe/Jurkat_PBIT_5h_10uM_2.fastq.gz

[Sat Apr 17 13:59:04 2021]
rule gunzip_extra:
    input: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.18.fa.gz
    output: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.18.fa
    log: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.18.fa.log
    jobid: 3530
    benchmark: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.18.fa.benchmark.tsv
    reason: Missing output files: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.18.fa; Input files updated by another job: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.18.fa.gz
    wildcards: tool=gunzip/, extra=to-stdout, filler=wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.18.fa

gunzip --to-stdout out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.18.fa.gz > out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.18.fa 2> out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.18.fa.log

[Sat Apr 17 13:59:04 2021]
rule cat:
    input: out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L001_R2_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L002_R2_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L003_R2_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L004_R2_001.fastq.gz
    output: out/cat/merge-nexsteq500-pe/Loucy_DMSO_5h_2.fastq.gz
    jobid: 3544
    reason: Missing output files: out/cat/merge-nexsteq500-pe/Loucy_DMSO_5h_2.fastq.gz; Input files updated by another job: out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L004_R2_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L001_R2_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L003_R2_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L002_R2_001.fastq.gz
    wildcards: cat_id=merge-nexsteq500-pe/Loucy_DMSO_5h_2.fastq.gz

cat out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L001_R2_001.fastq.gz out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L002_R2_001.fastq.gz out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L003_R2_001.fastq.gz out/ln/updir/mw/inp/fastq/run189/S001843_Loucy_PBIT_5h_DMSO-60064/Loucy-PBIT-5h-DMSO_S5_L004_R2_001.fastq.gz > out/cat/merge-nexsteq500-pe/Loucy_DMSO_5h_2.fastq.gz

[Sat Apr 17 13:59:04 2021]
rule sort_extra:
    input: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_LC_TH91_H3K4me3_S010Q7H1.bed
    output: out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_LC_TH91_H3K4me3_S010Q7H1.bed
    jobid: 2203
    reason: Missing output files: out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_LC_TH91_H3K4me3_S010Q7H1.bed; Input files updated by another job: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_LC_TH91_H3K4me3_S010Q7H1.bed
    wildcards: tool=sort/, extra=_-u, filler=ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_LC_TH91_H3K4me3_S010Q7H1.bed

LC_ALL=C; sort  -u out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_LC_TH91_H3K4me3_S010Q7H1.bed > out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_LC_TH91_H3K4me3_S010Q7H1.bed

[Sat Apr 17 13:59:04 2021]
rule gunzip_extra:
    input: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.20.fa.gz
    output: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.20.fa
    log: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.20.fa.log
    jobid: 3532
    benchmark: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.20.fa.benchmark.tsv
    reason: Missing output files: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.20.fa; Input files updated by another job: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.20.fa.gz
    wildcards: tool=gunzip/, extra=to-stdout, filler=wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.20.fa

gunzip --to-stdout out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.20.fa.gz > out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.20.fa 2> out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.20.fa.log

[Sat Apr 17 13:59:04 2021]
rule gunzip_extra:
    input: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.9.fa.gz
    output: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.9.fa
    log: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.9.fa.log
    jobid: 3521
    benchmark: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.9.fa.benchmark.tsv
    reason: Missing output files: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.9.fa; Input files updated by another job: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.9.fa.gz
    wildcards: tool=gunzip/, extra=to-stdout, filler=wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.9.fa

gunzip --to-stdout out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.9.fa.gz > out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.9.fa 2> out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.9.fa.log

[Sat Apr 17 13:59:04 2021]
rule sort_extra:
    input: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD4_TH91_H3K4me3_S010R5H1.bed
    output: out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD4_TH91_H3K4me3_S010R5H1.bed
    jobid: 329
    reason: Missing output files: out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD4_TH91_H3K4me3_S010R5H1.bed; Input files updated by another job: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD4_TH91_H3K4me3_S010R5H1.bed
    wildcards: tool=sort/, extra=_-u, filler=ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD4_TH91_H3K4me3_S010R5H1.bed

LC_ALL=C; sort  -u out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD4_TH91_H3K4me3_S010R5H1.bed > out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD4_TH91_H3K4me3_S010R5H1.bed

[Sat Apr 17 13:59:04 2021]
rule gunzip_extra:
    input: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.X.fa.gz
    output: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.X.fa
    log: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.X.fa.log
    jobid: 3535
    benchmark: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.X.fa.benchmark.tsv
    reason: Missing output files: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.X.fa; Input files updated by another job: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.X.fa.gz
    wildcards: tool=gunzip/, extra=to-stdout, filler=wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.X.fa

gunzip --to-stdout out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.X.fa.gz > out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.X.fa 2> out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.X.fa.log

[Sat Apr 17 13:59:04 2021]
rule cat:
    input: out/ln/updir/mw/inp/fastq/run204/S002104_Loucy_PBIT_24h_10uM-72078/Loucy-PBIT-24h-10uM_S7_L001_R1_001.fastq.gz, out/ln/updir/mw/inp/fastq/run204/S002104_Loucy_PBIT_24h_10uM-72078/Loucy-PBIT-24h-10uM_S7_L002_R1_001.fastq.gz, out/ln/updir/mw/inp/fastq/run204/S002104_Loucy_PBIT_24h_10uM-72078/Loucy-PBIT-24h-10uM_S7_L003_R1_001.fastq.gz, out/ln/updir/mw/inp/fastq/run204/S002104_Loucy_PBIT_24h_10uM-72078/Loucy-PBIT-24h-10uM_S7_L004_R1_001.fastq.gz
    output: out/cat/merge-nexsteq500-se/Loucy_PBIT_24h_10uM.fastq.gz
    jobid: 3547
    reason: Missing output files: out/cat/merge-nexsteq500-se/Loucy_PBIT_24h_10uM.fastq.gz; Input files updated by another job: out/ln/updir/mw/inp/fastq/run204/S002104_Loucy_PBIT_24h_10uM-72078/Loucy-PBIT-24h-10uM_S7_L003_R1_001.fastq.gz, out/ln/updir/mw/inp/fastq/run204/S002104_Loucy_PBIT_24h_10uM-72078/Loucy-PBIT-24h-10uM_S7_L004_R1_001.fastq.gz, out/ln/updir/mw/inp/fastq/run204/S002104_Loucy_PBIT_24h_10uM-72078/Loucy-PBIT-24h-10uM_S7_L002_R1_001.fastq.gz, out/ln/updir/mw/inp/fastq/run204/S002104_Loucy_PBIT_24h_10uM-72078/Loucy-PBIT-24h-10uM_S7_L001_R1_001.fastq.gz
    wildcards: cat_id=merge-nexsteq500-se/Loucy_PBIT_24h_10uM.fastq.gz

cat out/ln/updir/mw/inp/fastq/run204/S002104_Loucy_PBIT_24h_10uM-72078/Loucy-PBIT-24h-10uM_S7_L001_R1_001.fastq.gz out/ln/updir/mw/inp/fastq/run204/S002104_Loucy_PBIT_24h_10uM-72078/Loucy-PBIT-24h-10uM_S7_L002_R1_001.fastq.gz out/ln/updir/mw/inp/fastq/run204/S002104_Loucy_PBIT_24h_10uM-72078/Loucy-PBIT-24h-10uM_S7_L003_R1_001.fastq.gz out/ln/updir/mw/inp/fastq/run204/S002104_Loucy_PBIT_24h_10uM-72078/Loucy-PBIT-24h-10uM_S7_L004_R1_001.fastq.gz > out/cat/merge-nexsteq500-se/Loucy_PBIT_24h_10uM.fastq.gz

[Sat Apr 17 13:59:04 2021]
rule gunzip_extra:
    input: out/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt.gz
    output: out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt
    log: out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt.log
    jobid: 36
    benchmark: out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt.benchmark.tsv
    reason: Missing output files: out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt; Input files updated by another job: out/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt.gz
    wildcards: tool=gunzip/, extra=to-stdout, filler=wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt

gunzip --to-stdout out/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt.gz > out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt 2> out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt.log

[Sat Apr 17 13:59:04 2021]
rule sort_extra:
    input: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_EC_TH91_H3K4me3_S010NDH1.bed
    output: out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_EC_TH91_H3K4me3_S010NDH1.bed
    jobid: 323
    reason: Missing output files: out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_EC_TH91_H3K4me3_S010NDH1.bed; Input files updated by another job: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_EC_TH91_H3K4me3_S010NDH1.bed
    wildcards: tool=sort/, extra=_-u, filler=ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_EC_TH91_H3K4me3_S010NDH1.bed

LC_ALL=C; sort  -u out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_EC_TH91_H3K4me3_S010NDH1.bed > out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_EC_TH91_H3K4me3_S010NDH1.bed

[Sat Apr 17 13:59:04 2021]
rule tar_xvzf_igenome:
    input: out/wget/http/igenomes.illumina.com.s3-website-us-east-1.amazonaws.com/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz
    output: out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.5.x/genome.fa.amb, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.5.x/genome.fa.sa, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.5.x/genome.fa.bwt, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.5.x/genome.fa.ann, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.5.x/genome.fa.rbwt, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.5.x/genome.fa.pac, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.5.x/genome.fa.rpac, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.5.x/genome.fa.rsa, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/genome.fa.amb, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/genome.fa.sa, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/genome.fa.bwt, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/genome.fa.ann, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/genome.fa.pac, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome.2.ebwt, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome.rev.2.ebwt, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome.1.ebwt, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome.3.ebwt, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome.rev.1.ebwt, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome.4.ebwt, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/GenomeSize.xml, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.dict, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa.fai, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/AbundantSequences/polyA.fa, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/AbundantSequences/chrM.fa, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/AbundantSequences/polyC.fa, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/AbundantSequences/adapter_contam1.fa, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/AbundantSequences/phix.fa
    jobid: 3400
    reason: Missing output files: out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2; Input files updated by another job: out/wget/http/igenomes.illumina.com.s3-website-us-east-1.amazonaws.com/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz
    wildcards: specie=Homo_sapiens, source=UCSC, index=hg19


        tar -xvzf out/wget/http/igenomes.illumina.com.s3-website-us-east-1.amazonaws.com/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz --directory out/tar/xvzf_igenome
        touch out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2 out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2 out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2 out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2 out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2 out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2 out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.5.x/genome.fa.amb out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.5.x/genome.fa.sa out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.5.x/genome.fa.bwt out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.5.x/genome.fa.ann out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.5.x/genome.fa.rbwt out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.5.x/genome.fa.pac out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.5.x/genome.fa.rpac out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.5.x/genome.fa.rsa out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/genome.fa.amb out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/genome.fa.sa out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/genome.fa.bwt out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/genome.fa.ann out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/genome.fa.pac out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome.2.ebwt out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome.rev.2.ebwt out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome.1.ebwt out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome.3.ebwt out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome.rev.1.ebwt out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome.4.ebwt out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/GenomeSize.xml out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.dict out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa.fai out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/AbundantSequences/polyA.fa out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/AbundantSequences/chrM.fa out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/AbundantSequences/polyC.fa out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/AbundantSequences/adapter_contam1.fa out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/AbundantSequences/phix.fa # Without this touch the timestamp on the file makes it always older than the input tar archive, leading Snakemake to redo this rule every time.
        

[Sat Apr 17 13:59:04 2021]
rule sickle_pe_extra:
    input: out/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3_1.fastq.gz, out/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3_2.fastq.gz
    output: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3_2.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3_single.fastq.gz
    log: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.fastq.gz.log
    jobid: 3403
    reason: Missing output files: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3_2.fastq.gz; Input files updated by another job: out/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3_1.fastq.gz, out/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3_2.fastq.gz
    wildcards: tool=sickle/pe, extra=_-t_sanger_-q_20, filler=ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3, ext=fastq.gz

sickle pe -f out/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3_1.fastq.gz -r out/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3_2.fastq.gz -o out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3_1.fastq.gz -p out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3_2.fastq.gz -s out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3_single.fastq.gz  -t sanger -q 20 -g &> out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.fastq.gz.log

[Sat Apr 17 13:59:04 2021]
rule gunzip_extra:
    input: out/wget/ftp/ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz
    output: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf
    log: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.log
    jobid: 2383
    benchmark: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.benchmark.tsv
    reason: Missing output files: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf; Input files updated by another job: out/wget/ftp/ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz
    wildcards: tool=gunzip/, extra=to-stdout, filler=wget/ftp/ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf

gunzip --to-stdout out/wget/ftp/ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz > out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf 2> out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.log

[Sat Apr 17 13:59:04 2021]
rule sort_extra:
    input: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_LC_TH91_H3K4me3_S010Q7H1.bed
    output: out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_LC_TH91_H3K4me3_S010Q7H1.bed
    jobid: 331
    reason: Missing output files: out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_LC_TH91_H3K4me3_S010Q7H1.bed; Input files updated by another job: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_LC_TH91_H3K4me3_S010Q7H1.bed
    wildcards: tool=sort/, extra=_-u, filler=ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_LC_TH91_H3K4me3_S010Q7H1.bed

LC_ALL=C; sort  -u out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_LC_TH91_H3K4me3_S010Q7H1.bed > out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_LC_TH91_H3K4me3_S010Q7H1.bed

[Sat Apr 17 13:59:04 2021]
rule tail_extra:
    input: out/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.BedGraph
    output: out/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.BedGraph
    log: out/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.BedGraph.log
    jobid: 3318
    reason: Missing output files: out/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.BedGraph; Input files updated by another job: out/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.BedGraph
    wildcards: tool=tail/, extra=_-n+2, filler=igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.BedGraph

tail  -n+2 out/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.BedGraph > out/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.BedGraph 2> out/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.BedGraph.log

[Sat Apr 17 13:59:04 2021]
rule gunzip_extra:
    input: out/wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf.gz
    output: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf
    log: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf.log
    jobid: 3413
    benchmark: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf.benchmark.tsv
    reason: Missing output files: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf; Input files updated by another job: out/wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf.gz
    wildcards: tool=gunzip/, extra=to-stdout, filler=wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf

gunzip --to-stdout out/wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf.gz > out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf 2> out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf.log

[Sat Apr 17 13:59:04 2021]
rule gunzip_extra:
    input: out/wget/ftp/ftp.ensembl.org/pub/release-100/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.28.dna_sm.toplevel.fa.gz
    output: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-100/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.28.dna_sm.toplevel.fa
    log: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-100/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.28.dna_sm.toplevel.fa.log
    jobid: 3451
    benchmark: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-100/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.28.dna_sm.toplevel.fa.benchmark.tsv
    reason: Missing output files: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-100/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.28.dna_sm.toplevel.fa; Input files updated by another job: out/wget/ftp/ftp.ensembl.org/pub/release-100/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.28.dna_sm.toplevel.fa.gz
    wildcards: tool=gunzip/, extra=to-stdout, filler=wget/ftp/ftp.ensembl.org/pub/release-100/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.28.dna_sm.toplevel.fa

gunzip --to-stdout out/wget/ftp/ftp.ensembl.org/pub/release-100/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.28.dna_sm.toplevel.fa.gz > out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-100/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.28.dna_sm.toplevel.fa 2> out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-100/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.28.dna_sm.toplevel.fa.log

[Sat Apr 17 13:59:04 2021]
rule sickle_pe_extra:
    input: out/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3_1.fastq.gz, out/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3_2.fastq.gz
    output: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3_2.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3_single.fastq.gz
    log: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.fastq.gz.log
    jobid: 3399
    reason: Missing output files: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3_2.fastq.gz; Input files updated by another job: out/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3_2.fastq.gz, out/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3_1.fastq.gz
    wildcards: tool=sickle/pe, extra=_-t_sanger_-q_20, filler=ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3, ext=fastq.gz

sickle pe -f out/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3_1.fastq.gz -r out/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3_2.fastq.gz -o out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3_1.fastq.gz -p out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3_2.fastq.gz -s out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3_single.fastq.gz  -t sanger -q 20 -g &> out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.fastq.gz.log

[Sat Apr 17 13:59:04 2021]
rule cat:
    input: out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L001_R1_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L002_R1_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L003_R1_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L004_R1_001.fastq.gz
    output: out/cat/merge-nexsteq500-pe/Jurkat_PBIT_5h_10uM_1.fastq.gz
    jobid: 3539
    reason: Missing output files: out/cat/merge-nexsteq500-pe/Jurkat_PBIT_5h_10uM_1.fastq.gz; Input files updated by another job: out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L004_R1_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L001_R1_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L003_R1_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L002_R1_001.fastq.gz
    wildcards: cat_id=merge-nexsteq500-pe/Jurkat_PBIT_5h_10uM_1.fastq.gz

cat out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L001_R1_001.fastq.gz out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L002_R1_001.fastq.gz out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L003_R1_001.fastq.gz out/ln/updir/mw/inp/fastq/run189/S001834_Jurkat_PBIT_5h_10uM-60063/Jurkat-PBIT-5h-10uM_S4_L004_R1_001.fastq.gz > out/cat/merge-nexsteq500-pe/Jurkat_PBIT_5h_10uM_1.fastq.gz

[Sat Apr 17 13:59:04 2021]
rule sickle_pe_extra:
    input: out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3_1.fastq.gz, out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3_2.fastq.gz
    output: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3_2.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3_single.fastq.gz
    log: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.fastq.gz.log
    jobid: 3410
    reason: Missing output files: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3_2.fastq.gz; Input files updated by another job: out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3_1.fastq.gz, out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3_2.fastq.gz
    wildcards: tool=sickle/pe, extra=_-t_sanger_-q_20, filler=ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3, ext=fastq.gz

sickle pe -f out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3_1.fastq.gz -r out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3_2.fastq.gz -o out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3_1.fastq.gz -p out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3_2.fastq.gz -s out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3_single.fastq.gz  -t sanger -q 20 -g &> out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.fastq.gz.log

[Sat Apr 17 13:59:04 2021]
rule gunzip_extra:
    input: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.nonchromosomal.fa.gz
    output: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.nonchromosomal.fa
    log: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.nonchromosomal.fa.log
    jobid: 3538
    benchmark: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.nonchromosomal.fa.benchmark.tsv
    reason: Missing output files: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.nonchromosomal.fa; Input files updated by another job: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.nonchromosomal.fa.gz
    wildcards: tool=gunzip/, extra=to-stdout, filler=wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.nonchromosomal.fa

gunzip --to-stdout out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.nonchromosomal.fa.gz > out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.nonchromosomal.fa 2> out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.nonchromosomal.fa.log

[Sat Apr 17 13:59:04 2021]
rule gunzip_extra:
    input: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.Y.fa.gz
    output: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.Y.fa
    log: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.Y.fa.log
    jobid: 3536
    benchmark: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.Y.fa.benchmark.tsv
    reason: Missing output files: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.Y.fa; Input files updated by another job: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.Y.fa.gz
    wildcards: tool=gunzip/, extra=to-stdout, filler=wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.Y.fa

gunzip --to-stdout out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.Y.fa.gz > out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.Y.fa 2> out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.Y.fa.log

[Sat Apr 17 13:59:04 2021]
rule gunzip_extra:
    input: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.11.fa.gz
    output: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.11.fa
    log: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.11.fa.log
    jobid: 3523
    benchmark: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.11.fa.benchmark.tsv
    reason: Missing output files: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.11.fa; Input files updated by another job: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.11.fa.gz
    wildcards: tool=gunzip/, extra=to-stdout, filler=wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.11.fa

gunzip --to-stdout out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.11.fa.gz > out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.11.fa 2> out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.11.fa.log

[Sat Apr 17 13:59:04 2021]
rule gunzip_extra:
    input: out/wget/https/ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.gtf.gz
    output: out/gunzip/to-stdout/wget/https/ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.gtf
    log: out/gunzip/to-stdout/wget/https/ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.gtf.log
    jobid: 3395
    benchmark: out/gunzip/to-stdout/wget/https/ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.gtf.benchmark.tsv
    reason: Missing output files: out/gunzip/to-stdout/wget/https/ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.gtf; Input files updated by another job: out/wget/https/ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.gtf.gz
    wildcards: tool=gunzip/, extra=to-stdout, filler=wget/https/ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.gtf

gunzip --to-stdout out/wget/https/ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.gtf.gz > out/gunzip/to-stdout/wget/https/ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.gtf 2> out/gunzip/to-stdout/wget/https/ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.gtf.log

[Sat Apr 17 13:59:04 2021]
rule cat:
    input: out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L001_R2_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L002_R2_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L003_R2_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L004_R2_001.fastq.gz
    output: out/cat/merge-nexsteq500-pe/Jurkat_PBIT_24h_10uM_2.fastq.gz
    jobid: 3542
    reason: Missing output files: out/cat/merge-nexsteq500-pe/Jurkat_PBIT_24h_10uM_2.fastq.gz; Input files updated by another job: out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L003_R2_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L001_R2_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L002_R2_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L004_R2_001.fastq.gz
    wildcards: cat_id=merge-nexsteq500-pe/Jurkat_PBIT_24h_10uM_2.fastq.gz

cat out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L001_R2_001.fastq.gz out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L002_R2_001.fastq.gz out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L003_R2_001.fastq.gz out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L004_R2_001.fastq.gz > out/cat/merge-nexsteq500-pe/Jurkat_PBIT_24h_10uM_2.fastq.gz

[Sat Apr 17 13:59:04 2021]
rule gunzip_extra:
    input: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.10.fa.gz
    output: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.10.fa
    log: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.10.fa.log
    jobid: 3522
    benchmark: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.10.fa.benchmark.tsv
    reason: Missing output files: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.10.fa; Input files updated by another job: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.10.fa.gz
    wildcards: tool=gunzip/, extra=to-stdout, filler=wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.10.fa

gunzip --to-stdout out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.10.fa.gz > out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.10.fa 2> out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.10.fa.log

[Sat Apr 17 13:59:04 2021]
rule gunzip_extra:
    input: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.7.fa.gz
    output: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.7.fa
    log: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.7.fa.log
    jobid: 3519
    benchmark: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.7.fa.benchmark.tsv
    reason: Missing output files: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.7.fa; Input files updated by another job: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.7.fa.gz
    wildcards: tool=gunzip/, extra=to-stdout, filler=wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.7.fa

gunzip --to-stdout out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.7.fa.gz > out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.7.fa 2> out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.7.fa.log

[Sat Apr 17 13:59:04 2021]
rule sickle_pe_extra:
    input: out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3_1.fastq.gz, out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3_2.fastq.gz
    output: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3_2.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3_single.fastq.gz
    log: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.fastq.gz.log
    jobid: 3406
    reason: Missing output files: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3_2.fastq.gz; Input files updated by another job: out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3_2.fastq.gz, out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3_1.fastq.gz
    wildcards: tool=sickle/pe, extra=_-t_sanger_-q_20, filler=ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3, ext=fastq.gz

sickle pe -f out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3_1.fastq.gz -r out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3_2.fastq.gz -o out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3_1.fastq.gz -p out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3_2.fastq.gz -s out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3_single.fastq.gz  -t sanger -q 20 -g &> out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.fastq.gz.log

[Sat Apr 17 13:59:04 2021]
rule gunzip_extra:
    input: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.1.fa.gz
    output: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.1.fa
    log: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.1.fa.log
    jobid: 3513
    benchmark: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.1.fa.benchmark.tsv
    reason: Missing output files: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.1.fa; Input files updated by another job: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.1.fa.gz
    wildcards: tool=gunzip/, extra=to-stdout, filler=wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.1.fa

gunzip --to-stdout out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.1.fa.gz > out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.1.fa 2> out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.1.fa.log

[Sat Apr 17 13:59:04 2021]
rule tail_extra:
    input: out/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.BedGraph
    output: out/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.BedGraph
    log: out/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.BedGraph.log
    jobid: 3319
    reason: Missing output files: out/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.BedGraph; Input files updated by another job: out/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.BedGraph
    wildcards: tool=tail/, extra=_-n+2, filler=igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.BedGraph

tail  -n+2 out/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.BedGraph > out/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.BedGraph 2> out/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.BedGraph.log

[Sat Apr 17 13:59:04 2021]
rule tail_extra:
    input: out/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.BedGraph
    output: out/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.BedGraph
    log: out/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.BedGraph.log
    jobid: 3320
    reason: Missing output files: out/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.BedGraph; Input files updated by another job: out/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.BedGraph
    wildcards: tool=tail/, extra=_-n+2, filler=igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.BedGraph

tail  -n+2 out/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.BedGraph > out/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.BedGraph 2> out/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.BedGraph.log

[Sat Apr 17 13:59:04 2021]
rule gunzip_extra:
    input: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.17.fa.gz
    output: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.17.fa
    log: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.17.fa.log
    jobid: 3529
    benchmark: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.17.fa.benchmark.tsv
    reason: Missing output files: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.17.fa; Input files updated by another job: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.17.fa.gz
    wildcards: tool=gunzip/, extra=to-stdout, filler=wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.17.fa

gunzip --to-stdout out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.17.fa.gz > out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.17.fa 2> out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.17.fa.log

[Sat Apr 17 13:59:04 2021]
rule gunzip_extra:
    input: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.15.fa.gz
    output: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.15.fa
    log: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.15.fa.log
    jobid: 3527
    benchmark: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.15.fa.benchmark.tsv
    reason: Missing output files: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.15.fa; Input files updated by another job: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.15.fa.gz
    wildcards: tool=gunzip/, extra=to-stdout, filler=wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.15.fa

gunzip --to-stdout out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.15.fa.gz > out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.15.fa 2> out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.15.fa.log

[Sat Apr 17 13:59:04 2021]
rule sort_extra:
    input: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD4_TH91_H3K4me3_S010R5H1.bed
    output: out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD4_TH91_H3K4me3_S010R5H1.bed
    jobid: 2202
    reason: Missing output files: out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD4_TH91_H3K4me3_S010R5H1.bed; Input files updated by another job: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD4_TH91_H3K4me3_S010R5H1.bed
    wildcards: tool=sort/, extra=_-u, filler=ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD4_TH91_H3K4me3_S010R5H1.bed

LC_ALL=C; sort  -u out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD4_TH91_H3K4me3_S010R5H1.bed > out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD4_TH91_H3K4me3_S010R5H1.bed

[Sat Apr 17 13:59:04 2021]
rule sickle_pe_extra:
    input: out/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3_1.fastq.gz, out/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3_2.fastq.gz
    output: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3_2.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3_single.fastq.gz
    log: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.fastq.gz.log
    jobid: 3404
    reason: Missing output files: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3_2.fastq.gz; Input files updated by another job: out/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3_1.fastq.gz, out/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3_2.fastq.gz
    wildcards: tool=sickle/pe, extra=_-t_sanger_-q_20, filler=ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3, ext=fastq.gz

sickle pe -f out/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3_1.fastq.gz -r out/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3_2.fastq.gz -o out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3_1.fastq.gz -p out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3_2.fastq.gz -s out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3_single.fastq.gz  -t sanger -q 20 -g &> out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.fastq.gz.log

[Sat Apr 17 13:59:04 2021]
rule cat:
    input: out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L001_R2_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L002_R2_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L003_R2_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L004_R2_001.fastq.gz
    output: out/cat/merge-nexsteq500-pe/Loucy_PBIT_5h_10uM_2.fastq.gz
    jobid: 3546
    reason: Missing output files: out/cat/merge-nexsteq500-pe/Loucy_PBIT_5h_10uM_2.fastq.gz; Input files updated by another job: out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L003_R2_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L002_R2_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L001_R2_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L004_R2_001.fastq.gz
    wildcards: cat_id=merge-nexsteq500-pe/Loucy_PBIT_5h_10uM_2.fastq.gz

cat out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L001_R2_001.fastq.gz out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L002_R2_001.fastq.gz out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L003_R2_001.fastq.gz out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L004_R2_001.fastq.gz > out/cat/merge-nexsteq500-pe/Loucy_PBIT_5h_10uM_2.fastq.gz

[Sat Apr 17 13:59:04 2021]
rule cat:
    input: out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L001_R1_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L002_R1_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L003_R1_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L004_R1_001.fastq.gz
    output: out/cat/merge-nexsteq500-pe/Loucy_PBIT_5h_10uM_1.fastq.gz
    jobid: 3545
    reason: Missing output files: out/cat/merge-nexsteq500-pe/Loucy_PBIT_5h_10uM_1.fastq.gz; Input files updated by another job: out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L001_R1_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L002_R1_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L003_R1_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L004_R1_001.fastq.gz
    wildcards: cat_id=merge-nexsteq500-pe/Loucy_PBIT_5h_10uM_1.fastq.gz

cat out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L001_R1_001.fastq.gz out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L002_R1_001.fastq.gz out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L003_R1_001.fastq.gz out/ln/updir/mw/inp/fastq/run189/S001844_Loucy_PBIT_5h_10uM-60061/Loucy-PBIT-5h-10uM_S2_L004_R1_001.fastq.gz > out/cat/merge-nexsteq500-pe/Loucy_PBIT_5h_10uM_1.fastq.gz

[Sat Apr 17 13:59:04 2021]
rule gunzip_extra:
    input: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.16.fa.gz
    output: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.16.fa
    log: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.16.fa.log
    jobid: 3528
    benchmark: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.16.fa.benchmark.tsv
    reason: Missing output files: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.16.fa; Input files updated by another job: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.16.fa.gz
    wildcards: tool=gunzip/, extra=to-stdout, filler=wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.16.fa

gunzip --to-stdout out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.16.fa.gz > out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.16.fa 2> out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.16.fa.log

[Sat Apr 17 13:59:04 2021]
rule gunzip_extra:
    input: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.21.fa.gz
    output: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.21.fa
    log: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.21.fa.log
    jobid: 3533
    benchmark: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.21.fa.benchmark.tsv
    reason: Missing output files: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.21.fa; Input files updated by another job: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.21.fa.gz
    wildcards: tool=gunzip/, extra=to-stdout, filler=wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.21.fa

gunzip --to-stdout out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.21.fa.gz > out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.21.fa 2> out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.21.fa.log

[Sat Apr 17 13:59:04 2021]
rule sickle_pe_extra:
    input: out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3_1.fastq.gz, out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3_2.fastq.gz
    output: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3_2.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3_single.fastq.gz
    log: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.fastq.gz.log
    jobid: 3409
    reason: Missing output files: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3_2.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3_1.fastq.gz; Input files updated by another job: out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3_2.fastq.gz, out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3_1.fastq.gz
    wildcards: tool=sickle/pe, extra=_-t_sanger_-q_20, filler=ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3, ext=fastq.gz

sickle pe -f out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3_1.fastq.gz -r out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3_2.fastq.gz -o out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3_1.fastq.gz -p out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3_2.fastq.gz -s out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3_single.fastq.gz  -t sanger -q 20 -g &> out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.fastq.gz.log

[Sat Apr 17 13:59:04 2021]
rule gunzip_extra:
    input: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.MT.fa.gz
    output: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.MT.fa
    log: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.MT.fa.log
    jobid: 3537
    benchmark: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.MT.fa.benchmark.tsv
    reason: Missing output files: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.MT.fa; Input files updated by another job: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.MT.fa.gz
    wildcards: tool=gunzip/, extra=to-stdout, filler=wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.MT.fa

gunzip --to-stdout out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.MT.fa.gz > out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.MT.fa 2> out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.MT.fa.log

[Sat Apr 17 13:59:04 2021]
rule sort_extra:
    input: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_EC_TH91_H3K4me3_S010NDH1.bed
    output: out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_EC_TH91_H3K4me3_S010NDH1.bed
    jobid: 2204
    reason: Missing output files: out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_EC_TH91_H3K4me3_S010NDH1.bed; Input files updated by another job: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_EC_TH91_H3K4me3_S010NDH1.bed
    wildcards: tool=sort/, extra=_-u, filler=ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_EC_TH91_H3K4me3_S010NDH1.bed

LC_ALL=C; sort  -u out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_EC_TH91_H3K4me3_S010NDH1.bed > out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_EC_TH91_H3K4me3_S010NDH1.bed

[Sat Apr 17 13:59:04 2021]
rule gunzip_extra:
    input: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.2.fa.gz
    output: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.2.fa
    log: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.2.fa.log
    jobid: 3514
    benchmark: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.2.fa.benchmark.tsv
    reason: Missing output files: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.2.fa; Input files updated by another job: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.2.fa.gz
    wildcards: tool=gunzip/, extra=to-stdout, filler=wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.2.fa

gunzip --to-stdout out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.2.fa.gz > out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.2.fa 2> out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.2.fa.log

[Sat Apr 17 13:59:04 2021]
rule tail_extra:
    input: out/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.BedGraph
    output: out/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.BedGraph
    log: out/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.BedGraph.log
    jobid: 3317
    reason: Missing output files: out/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.BedGraph; Input files updated by another job: out/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.BedGraph
    wildcards: tool=tail/, extra=_-n+2, filler=igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.BedGraph

tail  -n+2 out/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.BedGraph > out/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.BedGraph 2> out/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.BedGraph.log

[Sat Apr 17 13:59:04 2021]
rule sort_extra:
    input: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD8_TH91_H3K4me3_S010S3H1.bed
    output: out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD8_TH91_H3K4me3_S010S3H1.bed
    jobid: 327
    reason: Missing output files: out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD8_TH91_H3K4me3_S010S3H1.bed; Input files updated by another job: out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD8_TH91_H3K4me3_S010S3H1.bed
    wildcards: tool=sort/, extra=_-u, filler=ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD8_TH91_H3K4me3_S010S3H1.bed

LC_ALL=C; sort  -u out/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD8_TH91_H3K4me3_S010S3H1.bed > out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD8_TH91_H3K4me3_S010S3H1.bed

[Sat Apr 17 13:59:04 2021]
rule cat:
    input: out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L001_R1_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L002_R1_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L003_R1_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L004_R1_001.fastq.gz
    output: out/cat/merge-nexsteq500-pe/Jurkat_PBIT_24h_10uM_1.fastq.gz
    jobid: 3541
    reason: Missing output files: out/cat/merge-nexsteq500-pe/Jurkat_PBIT_24h_10uM_1.fastq.gz; Input files updated by another job: out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L001_R1_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L003_R1_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L004_R1_001.fastq.gz, out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L002_R1_001.fastq.gz
    wildcards: cat_id=merge-nexsteq500-pe/Jurkat_PBIT_24h_10uM_1.fastq.gz

cat out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L001_R1_001.fastq.gz out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L002_R1_001.fastq.gz out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L003_R1_001.fastq.gz out/ln/updir/mw/inp/fastq/run189/S001842_Jurkat_PBIT_24h_10uM-60060/Jurkat-PBIT-24h-10uM_S1_L004_R1_001.fastq.gz > out/cat/merge-nexsteq500-pe/Jurkat_PBIT_24h_10uM_1.fastq.gz

[Sat Apr 17 13:59:04 2021]
rule gunzip_extra:
    input: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.4.fa.gz
    output: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.4.fa
    log: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.4.fa.log
    jobid: 3516
    benchmark: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.4.fa.benchmark.tsv
    reason: Missing output files: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.4.fa; Input files updated by another job: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.4.fa.gz
    wildcards: tool=gunzip/, extra=to-stdout, filler=wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.4.fa

gunzip --to-stdout out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.4.fa.gz > out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.4.fa 2> out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.4.fa.log

[Sat Apr 17 13:59:04 2021]
rule gunzip_extra:
    input: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.22.fa.gz
    output: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.22.fa
    log: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.22.fa.log
    jobid: 3534
    benchmark: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.22.fa.benchmark.tsv
    reason: Missing output files: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.22.fa; Input files updated by another job: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.22.fa.gz
    wildcards: tool=gunzip/, extra=to-stdout, filler=wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.22.fa

gunzip --to-stdout out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.22.fa.gz > out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.22.fa 2> out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.22.fa.log

[Sat Apr 17 13:59:04 2021]
rule gunzip_extra:
    input: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.13.fa.gz
    output: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.13.fa
    log: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.13.fa.log
    jobid: 3525
    benchmark: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.13.fa.benchmark.tsv
    reason: Missing output files: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.13.fa; Input files updated by another job: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.13.fa.gz
    wildcards: tool=gunzip/, extra=to-stdout, filler=wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.13.fa

gunzip --to-stdout out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.13.fa.gz > out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.13.fa 2> out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.13.fa.log

[Sat Apr 17 13:59:04 2021]
rule gunzip_extra:
    input: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.8.fa.gz
    output: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.8.fa
    log: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.8.fa.log
    jobid: 3520
    benchmark: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.8.fa.benchmark.tsv
    reason: Missing output files: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.8.fa; Input files updated by another job: out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.8.fa.gz
    wildcards: tool=gunzip/, extra=to-stdout, filler=wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.8.fa

gunzip --to-stdout out/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.8.fa.gz > out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.8.fa 2> out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.8.fa.log

[Sat Apr 17 13:59:04 2021]
localrule ln_alias:
    input: out/cat/merge-nexsteq500-se/Loucy_PBIT_24h_10uM.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM.fastq.gz
    jobid: 3482
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM.fastq.gz; Input files updated by another job: out/cat/merge-nexsteq500-se/Loucy_PBIT_24h_10uM.fastq.gz
    wildcards: id=sst/all_samples/fastq/Loucy_PBIT_24h_10uM.fastq.gz
    priority: 10

ln -srf 'out/cat/merge-nexsteq500-se/Loucy_PBIT_24h_10uM.fastq.gz' out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM.fastq.gz

[Sat Apr 17 13:59:04 2021]
localrule ln_alias:
    input: out/cat/merge-nexsteq500-pe/Jurkat_PBIT_5h_10uM_2.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM_2.fastq.gz
    jobid: 3475
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM_2.fastq.gz; Input files updated by another job: out/cat/merge-nexsteq500-pe/Jurkat_PBIT_5h_10uM_2.fastq.gz
    wildcards: id=sst/all_samples/fastq/Jurkat_PBIT_5h_10uM_2.fastq.gz
    priority: 10

ln -srf 'out/cat/merge-nexsteq500-pe/Jurkat_PBIT_5h_10uM_2.fastq.gz' out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM_2.fastq.gz

[Sat Apr 17 13:59:04 2021]
localrule ln_alias:
    input: out/cat/merge-nexsteq500-pe/Loucy_PBIT_5h_10uM_1.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM_1.fastq.gz
    jobid: 3480
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM_1.fastq.gz; Input files updated by another job: out/cat/merge-nexsteq500-pe/Loucy_PBIT_5h_10uM_1.fastq.gz
    wildcards: id=sst/all_samples/fastq/Loucy_PBIT_5h_10uM_1.fastq.gz
    priority: 10

ln -srf 'out/cat/merge-nexsteq500-pe/Loucy_PBIT_5h_10uM_1.fastq.gz' out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM_1.fastq.gz

[Sat Apr 17 13:59:04 2021]
localrule ln_alias:
    input: out/cat/merge-nexsteq500-pe/Jurkat_DMSO_5h_2.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h_2.fastq.gz
    jobid: 3471
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h_2.fastq.gz; Input files updated by another job: out/cat/merge-nexsteq500-pe/Jurkat_DMSO_5h_2.fastq.gz
    wildcards: id=sst/all_samples/fastq/Jurkat_DMSO_5h_2.fastq.gz
    priority: 10

ln -srf 'out/cat/merge-nexsteq500-pe/Jurkat_DMSO_5h_2.fastq.gz' out/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h_2.fastq.gz

[Sat Apr 17 13:59:04 2021]
localrule ln_alias:
    input: out/cat/merge-nexsteq500-pe/Jurkat_PBIT_24h_10uM_1.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM_1.fastq.gz
    jobid: 3476
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM_1.fastq.gz; Input files updated by another job: out/cat/merge-nexsteq500-pe/Jurkat_PBIT_24h_10uM_1.fastq.gz
    wildcards: id=sst/all_samples/fastq/Jurkat_PBIT_24h_10uM_1.fastq.gz
    priority: 10

ln -srf 'out/cat/merge-nexsteq500-pe/Jurkat_PBIT_24h_10uM_1.fastq.gz' out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM_1.fastq.gz

[Sat Apr 17 13:59:04 2021]
localrule ln_alias:
    input: out/cat/merge-nexsteq500-pe/Jurkat_PBIT_5h_10uM_1.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM_1.fastq.gz
    jobid: 3474
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM_1.fastq.gz; Input files updated by another job: out/cat/merge-nexsteq500-pe/Jurkat_PBIT_5h_10uM_1.fastq.gz
    wildcards: id=sst/all_samples/fastq/Jurkat_PBIT_5h_10uM_1.fastq.gz
    priority: 10

ln -srf 'out/cat/merge-nexsteq500-pe/Jurkat_PBIT_5h_10uM_1.fastq.gz' out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM_1.fastq.gz

[Sat Apr 17 13:59:04 2021]
localrule ln_alias:
    input: out/cat/merge-nexsteq500-pe/Jurkat_PBIT_24h_10uM_2.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM_2.fastq.gz
    jobid: 3477
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM_2.fastq.gz; Input files updated by another job: out/cat/merge-nexsteq500-pe/Jurkat_PBIT_24h_10uM_2.fastq.gz
    wildcards: id=sst/all_samples/fastq/Jurkat_PBIT_24h_10uM_2.fastq.gz
    priority: 10

ln -srf 'out/cat/merge-nexsteq500-pe/Jurkat_PBIT_24h_10uM_2.fastq.gz' out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM_2.fastq.gz

[Sat Apr 17 13:59:04 2021]
localrule ln_alias:
    input: out/cat/merge-nexsteq500-pe/Loucy_DMSO_5h_2.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h_2.fastq.gz
    jobid: 3479
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h_2.fastq.gz; Input files updated by another job: out/cat/merge-nexsteq500-pe/Loucy_DMSO_5h_2.fastq.gz
    wildcards: id=sst/all_samples/fastq/Loucy_DMSO_5h_2.fastq.gz
    priority: 10

ln -srf 'out/cat/merge-nexsteq500-pe/Loucy_DMSO_5h_2.fastq.gz' out/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h_2.fastq.gz

[Sat Apr 17 13:59:04 2021]
localrule ln_alias:
    input: out/cat/merge-nexsteq500-pe/Jurkat_DMSO_5h_1.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h_1.fastq.gz
    jobid: 3470
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h_1.fastq.gz; Input files updated by another job: out/cat/merge-nexsteq500-pe/Jurkat_DMSO_5h_1.fastq.gz
    wildcards: id=sst/all_samples/fastq/Jurkat_DMSO_5h_1.fastq.gz
    priority: 10

ln -srf 'out/cat/merge-nexsteq500-pe/Jurkat_DMSO_5h_1.fastq.gz' out/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h_1.fastq.gz

[Sat Apr 17 13:59:04 2021]
localrule ln_alias:
    input: out/cat/merge-nexsteq500-pe/Loucy_PBIT_5h_10uM_2.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM_2.fastq.gz
    jobid: 3481
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM_2.fastq.gz; Input files updated by another job: out/cat/merge-nexsteq500-pe/Loucy_PBIT_5h_10uM_2.fastq.gz
    wildcards: id=sst/all_samples/fastq/Loucy_PBIT_5h_10uM_2.fastq.gz
    priority: 10

ln -srf 'out/cat/merge-nexsteq500-pe/Loucy_PBIT_5h_10uM_2.fastq.gz' out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM_2.fastq.gz

[Sat Apr 17 13:59:04 2021]
localrule ln_alias:
    input: out/cat/merge-nexsteq500-pe/Loucy_DMSO_5h_1.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h_1.fastq.gz
    jobid: 3478
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h_1.fastq.gz; Input files updated by another job: out/cat/merge-nexsteq500-pe/Loucy_DMSO_5h_1.fastq.gz
    wildcards: id=sst/all_samples/fastq/Loucy_DMSO_5h_1.fastq.gz
    priority: 10

ln -srf 'out/cat/merge-nexsteq500-pe/Loucy_DMSO_5h_1.fastq.gz' out/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h_1.fastq.gz

[Sat Apr 17 13:59:04 2021]
rule sickle_se_extra:
    input: out/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.fastq.gz
    output: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.fastq.gz
    log: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.fastq.gz.log
    jobid: 3570
    reason: Missing output files: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.fastq.gz; Input files updated by another job: out/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.fastq.gz
    wildcards: tool=sickle/se, extra=_-t_sanger_-q_20, filler=ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3, ext=fastq.gz

sickle se -f out/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.fastq.gz  -t sanger -q 20 -g -o out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.fastq.gz &> out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.fastq.gz.log

[Sat Apr 17 13:59:04 2021]
rule bowtie2_build:
    input: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-100/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.28.dna_sm.toplevel.fa
    output: out/bowtie2-build/fa-genome-BDGP6.1.bt2, out/bowtie2-build/fa-genome-BDGP6.2.bt2, out/bowtie2-build/fa-genome-BDGP6.3.bt2, out/bowtie2-build/fa-genome-BDGP6.4.bt2, out/bowtie2-build/fa-genome-BDGP6.rev.1.bt2, out/bowtie2-build/fa-genome-BDGP6.rev.2.bt2
    jobid: 3401
    reason: Missing output files: out/bowtie2-build/fa-genome-BDGP6.rev.1.bt2, out/bowtie2-build/fa-genome-BDGP6.2.bt2, out/bowtie2-build/fa-genome-BDGP6.3.bt2, out/bowtie2-build/fa-genome-BDGP6.1.bt2, out/bowtie2-build/fa-genome-BDGP6.4.bt2, out/bowtie2-build/fa-genome-BDGP6.rev.2.bt2; Input files updated by another job: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-100/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.28.dna_sm.toplevel.fa
    wildcards: fa_genome_id=fa-genome-BDGP6
    threads: 2


        bowtie2-build --threads 2 out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-100/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.28.dna_sm.toplevel.fa out/bowtie2-build/fa-genome-BDGP6
        

[Sat Apr 17 13:59:04 2021]
rule bowtie2_paired_end_extra:
    input: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3_2.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2
    output: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.sam, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3/unmapped/single.fastq.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3/unmapped/pair.fastq.1.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3/unmapped/pair.fastq.2.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3/unmapped_single.fastq.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3/unmapped_pair1.fastq.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3/unmapped_pair2.fastq.gz
    log: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 3342
    reason: Missing output files: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.sam; Input files updated by another job: out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3_1.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3_2.fastq.gz
    wildcards: tool=bowtie2/pe, extra=, index=hg19, filler=sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    threads: 2


        bowtie2 -p 2 -x out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome            -1 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3_1.fastq.gz -2 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3_2.fastq.gz            --un-gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3/unmapped/single.fastq.gz            --un-conc-gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3/unmapped/pair.fastq.gz            -S out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.sam                        2> out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

        ln -srf out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3/unmapped/single.fastq.gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3/unmapped_single.fastq.gz
        ln -srf out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3/unmapped/pair.fastq.1.gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3/unmapped_pair1.fastq.gz
        ln -srf out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3/unmapped/pair.fastq.2.gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3/unmapped_pair2.fastq.gz
        

[Sat Apr 17 13:59:04 2021]
rule sickle_se_extra:
    input: out/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.fastq.gz
    output: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.fastq.gz
    log: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.fastq.gz.log
    jobid: 3678
    reason: Missing output files: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.fastq.gz; Input files updated by another job: out/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.fastq.gz
    wildcards: tool=sickle/se, extra=_-t_sanger_-q_20, filler=ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7, ext=fastq.gz

sickle se -f out/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.fastq.gz  -t sanger -q 20 -g -o out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.fastq.gz &> out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.fastq.gz.log

[Sat Apr 17 13:59:04 2021]
rule cat:
    input: out/ln/alias/sst/all_samples/fastq/Loucy_SRR5339376_H3K36me3.fastq.gz, out/ln/alias/sst/all_samples/fastq/Loucy_SRR5339377_H3K36me3.fastq.gz
    output: out/cat/merge-fastq-samples/Loucy_SRX2636361_H3K36me3.fastq.gz
    jobid: 3711
    reason: Missing output files: out/cat/merge-fastq-samples/Loucy_SRX2636361_H3K36me3.fastq.gz; Input files updated by another job: out/ln/alias/sst/all_samples/fastq/Loucy_SRR5339376_H3K36me3.fastq.gz, out/ln/alias/sst/all_samples/fastq/Loucy_SRR5339377_H3K36me3.fastq.gz
    wildcards: cat_id=merge-fastq-samples/Loucy_SRX2636361_H3K36me3.fastq.gz

cat out/ln/alias/sst/all_samples/fastq/Loucy_SRR5339376_H3K36me3.fastq.gz out/ln/alias/sst/all_samples/fastq/Loucy_SRR5339377_H3K36me3.fastq.gz > out/cat/merge-fastq-samples/Loucy_SRX2636361_H3K36me3.fastq.gz

[Sat Apr 17 13:59:04 2021]
rule bowtie2_paired_end_extra:
    input: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3_2.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2
    output: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.sam, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3/unmapped/single.fastq.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3/unmapped/pair.fastq.1.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3/unmapped/pair.fastq.2.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3/unmapped_single.fastq.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3/unmapped_pair1.fastq.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3/unmapped_pair2.fastq.gz
    log: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 3348
    reason: Missing output files: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.sam; Input files updated by another job: out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3_2.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3_1.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2
    wildcards: tool=bowtie2/pe, extra=, index=hg19, filler=sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    threads: 2


        bowtie2 -p 2 -x out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome            -1 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3_1.fastq.gz -2 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3_2.fastq.gz            --un-gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3/unmapped/single.fastq.gz            --un-conc-gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3/unmapped/pair.fastq.gz            -S out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.sam                        2> out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

        ln -srf out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3/unmapped/single.fastq.gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3/unmapped_single.fastq.gz
        ln -srf out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3/unmapped/pair.fastq.1.gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3/unmapped_pair1.fastq.gz
        ln -srf out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3/unmapped/pair.fastq.2.gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3/unmapped_pair2.fastq.gz
        

[Sat Apr 17 13:59:04 2021]
rule sort_extra:
    input: out/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.BedGraph
    output: out/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.BedGraph
    jobid: 2210
    reason: Missing output files: out/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.BedGraph; Input files updated by another job: out/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.BedGraph
    wildcards: tool=sort/, extra=_-k1,1_-k2,2n, filler=tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.BedGraph

LC_ALL=C; sort  -k1,1 -k2,2n out/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.BedGraph > out/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.BedGraph

[Sat Apr 17 13:59:04 2021]
rule bowtie2_paired_end_extra:
    input: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3_2.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2
    output: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.sam, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3/unmapped/single.fastq.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3/unmapped/pair.fastq.1.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3/unmapped/pair.fastq.2.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3/unmapped_single.fastq.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3/unmapped_pair1.fastq.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3/unmapped_pair2.fastq.gz
    log: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 3344
    reason: Missing output files: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.sam; Input files updated by another job: out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3_2.fastq.gz
    wildcards: tool=bowtie2/pe, extra=, index=hg19, filler=sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    threads: 2


        bowtie2 -p 2 -x out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome            -1 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3_1.fastq.gz -2 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3_2.fastq.gz            --un-gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3/unmapped/single.fastq.gz            --un-conc-gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3/unmapped/pair.fastq.gz            -S out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.sam                        2> out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

        ln -srf out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3/unmapped/single.fastq.gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3/unmapped_single.fastq.gz
        ln -srf out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3/unmapped/pair.fastq.1.gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3/unmapped_pair1.fastq.gz
        ln -srf out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3/unmapped/pair.fastq.2.gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3/unmapped_pair2.fastq.gz
        

[Sat Apr 17 13:59:04 2021]
rule cat:
    input: out/ln/alias/sst/all_samples/fastq/DND-41_SRR568235_H3K79me2.fastq.gz, out/ln/alias/sst/all_samples/fastq/DND-41_SRR568236_H3K79me2.fastq.gz
    output: out/cat/merge-fastq-samples/DND-41_SRX186665_H3K79me2.fastq.gz
    jobid: 3701
    reason: Missing output files: out/cat/merge-fastq-samples/DND-41_SRX186665_H3K79me2.fastq.gz; Input files updated by another job: out/ln/alias/sst/all_samples/fastq/DND-41_SRR568235_H3K79me2.fastq.gz, out/ln/alias/sst/all_samples/fastq/DND-41_SRR568236_H3K79me2.fastq.gz
    wildcards: cat_id=merge-fastq-samples/DND-41_SRX186665_H3K79me2.fastq.gz

cat out/ln/alias/sst/all_samples/fastq/DND-41_SRR568235_H3K79me2.fastq.gz out/ln/alias/sst/all_samples/fastq/DND-41_SRR568236_H3K79me2.fastq.gz > out/cat/merge-fastq-samples/DND-41_SRX186665_H3K79me2.fastq.gz

[Sat Apr 17 13:59:04 2021]
rule sickle_se_extra:
    input: out/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.fastq.gz
    output: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.fastq.gz
    log: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.fastq.gz.log
    jobid: 3677
    reason: Missing output files: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.fastq.gz; Input files updated by another job: out/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.fastq.gz
    wildcards: tool=sickle/se, extra=_-t_sanger_-q_20, filler=ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3, ext=fastq.gz

sickle se -f out/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.fastq.gz  -t sanger -q 20 -g -o out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.fastq.gz &> out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.fastq.gz.log

[Sat Apr 17 13:59:04 2021]
rule bowtie2_paired_end_extra:
    input: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3_2.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2
    output: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.sam, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3/unmapped/single.fastq.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3/unmapped/pair.fastq.1.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3/unmapped/pair.fastq.2.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3/unmapped_single.fastq.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3/unmapped_pair1.fastq.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3/unmapped_pair2.fastq.gz
    log: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 3354
    reason: Missing output files: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.sam; Input files updated by another job: out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3_1.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3_2.fastq.gz
    wildcards: tool=bowtie2/pe, extra=, index=hg19, filler=sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    threads: 2


        bowtie2 -p 2 -x out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome            -1 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3_1.fastq.gz -2 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3_2.fastq.gz            --un-gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3/unmapped/single.fastq.gz            --un-conc-gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3/unmapped/pair.fastq.gz            -S out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.sam                        2> out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

        ln -srf out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3/unmapped/single.fastq.gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3/unmapped_single.fastq.gz
        ln -srf out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3/unmapped/pair.fastq.1.gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3/unmapped_pair1.fastq.gz
        ln -srf out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3/unmapped/pair.fastq.2.gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3/unmapped_pair2.fastq.gz
        

[Sat Apr 17 13:59:04 2021]
rule sort_extra:
    input: out/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.BedGraph
    output: out/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.BedGraph
    jobid: 2212
    reason: Missing output files: out/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.BedGraph; Input files updated by another job: out/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.BedGraph
    wildcards: tool=sort/, extra=_-k1,1_-k2,2n, filler=tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.BedGraph

LC_ALL=C; sort  -k1,1 -k2,2n out/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.BedGraph > out/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.BedGraph

[Sat Apr 17 13:59:04 2021]
rule cat:
    input: out/ln/alias/sst/all_samples/fastq/DND-41_SRR568223_H3K36me3.fastq.gz, out/ln/alias/sst/all_samples/fastq/DND-41_SRR568224_H3K36me3.fastq.gz
    output: out/cat/merge-fastq-samples/DND-41_SRX186659_H3K36me3.fastq.gz
    jobid: 3700
    reason: Missing output files: out/cat/merge-fastq-samples/DND-41_SRX186659_H3K36me3.fastq.gz; Input files updated by another job: out/ln/alias/sst/all_samples/fastq/DND-41_SRR568223_H3K36me3.fastq.gz, out/ln/alias/sst/all_samples/fastq/DND-41_SRR568224_H3K36me3.fastq.gz
    wildcards: cat_id=merge-fastq-samples/DND-41_SRX186659_H3K36me3.fastq.gz

cat out/ln/alias/sst/all_samples/fastq/DND-41_SRR568223_H3K36me3.fastq.gz out/ln/alias/sst/all_samples/fastq/DND-41_SRR568224_H3K36me3.fastq.gz > out/cat/merge-fastq-samples/DND-41_SRX186659_H3K36me3.fastq.gz

[Sat Apr 17 13:59:04 2021]
rule bowtie2_paired_end_extra:
    input: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3_2.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2
    output: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.sam, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3/unmapped/single.fastq.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3/unmapped/pair.fastq.1.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3/unmapped/pair.fastq.2.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3/unmapped_single.fastq.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3/unmapped_pair1.fastq.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3/unmapped_pair2.fastq.gz
    log: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 3352
    reason: Missing output files: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.sam; Input files updated by another job: out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3_1.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3_2.fastq.gz
    wildcards: tool=bowtie2/pe, extra=, index=hg19, filler=sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    threads: 2


        bowtie2 -p 2 -x out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome            -1 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3_1.fastq.gz -2 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3_2.fastq.gz            --un-gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3/unmapped/single.fastq.gz            --un-conc-gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3/unmapped/pair.fastq.gz            -S out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.sam                        2> out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

        ln -srf out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3/unmapped/single.fastq.gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3/unmapped_single.fastq.gz
        ln -srf out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3/unmapped/pair.fastq.1.gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3/unmapped_pair1.fastq.gz
        ln -srf out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3/unmapped/pair.fastq.2.gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3/unmapped_pair2.fastq.gz
        

[Sat Apr 17 13:59:04 2021]
rule sickle_se_extra:
    input: out/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.fastq.gz
    output: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.fastq.gz
    log: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.fastq.gz.log
    jobid: 3574
    reason: Missing output files: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.fastq.gz; Input files updated by another job: out/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.fastq.gz
    wildcards: tool=sickle/se, extra=_-t_sanger_-q_20, filler=ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3, ext=fastq.gz

sickle se -f out/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.fastq.gz  -t sanger -q 20 -g -o out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.fastq.gz &> out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.fastq.gz.log

[Sat Apr 17 13:59:04 2021]
rule gtftk_select_by_key_key_value:
    input: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf
    output: out/gtftk/select_by_key_key-gene_biotype_value-protein_coding/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf
    jobid: 346
    reason: Missing output files: out/gtftk/select_by_key_key-gene_biotype_value-protein_coding/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf; Input files updated by another job: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf
    wildcards: key=gene_biotype, value=protein_coding, filler=gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87


        gtftk select_by_key             --inputfile out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf             --outputfile out/gtftk/select_by_key_key-gene_biotype_value-protein_coding/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf             --key gene_biotype             --value protein_coding
        

[Sat Apr 17 13:59:04 2021]
rule sort_extra:
    input: out/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.BedGraph
    output: out/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.BedGraph
    jobid: 2211
    reason: Missing output files: out/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.BedGraph; Input files updated by another job: out/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.BedGraph
    wildcards: tool=sort/, extra=_-k1,1_-k2,2n, filler=tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.BedGraph

LC_ALL=C; sort  -k1,1 -k2,2n out/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.BedGraph > out/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.BedGraph

[Sat Apr 17 13:59:04 2021]
rule bowtie2_paired_end_extra:
    input: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3_2.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2
    output: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.sam, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3/unmapped/single.fastq.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3/unmapped/pair.fastq.1.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3/unmapped/pair.fastq.2.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3/unmapped_single.fastq.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3/unmapped_pair1.fastq.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3/unmapped_pair2.fastq.gz
    log: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 3358
    reason: Missing output files: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.sam; Input files updated by another job: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3_1.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3_2.fastq.gz
    wildcards: tool=bowtie2/pe, extra=, index=hg19, filler=sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    threads: 2


        bowtie2 -p 2 -x out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome            -1 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3_1.fastq.gz -2 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3_2.fastq.gz            --un-gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3/unmapped/single.fastq.gz            --un-conc-gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3/unmapped/pair.fastq.gz            -S out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.sam                        2> out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

        ln -srf out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3/unmapped/single.fastq.gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3/unmapped_single.fastq.gz
        ln -srf out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3/unmapped/pair.fastq.1.gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3/unmapped_pair1.fastq.gz
        ln -srf out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3/unmapped/pair.fastq.2.gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3/unmapped_pair2.fastq.gz
        

[Sat Apr 17 13:59:04 2021]
rule sickle_se_extra:
    input: out/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.fastq.gz
    output: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.fastq.gz
    log: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.fastq.gz.log
    jobid: 3679
    reason: Missing output files: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.fastq.gz; Input files updated by another job: out/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.fastq.gz
    wildcards: tool=sickle/se, extra=_-t_sanger_-q_20, filler=ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3, ext=fastq.gz

sickle se -f out/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.fastq.gz  -t sanger -q 20 -g -o out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.fastq.gz &> out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.fastq.gz.log

[Sat Apr 17 13:59:04 2021]
rule bowtie2_paired_end_extra:
    input: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3_2.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2
    output: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.sam, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3/unmapped/single.fastq.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3/unmapped/pair.fastq.1.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3/unmapped/pair.fastq.2.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3/unmapped_single.fastq.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3/unmapped_pair1.fastq.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3/unmapped_pair2.fastq.gz
    log: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 3350
    reason: Missing output files: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.sam; Input files updated by another job: out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3_2.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3_1.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2
    wildcards: tool=bowtie2/pe, extra=, index=hg19, filler=sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    threads: 2


        bowtie2 -p 2 -x out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome            -1 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3_1.fastq.gz -2 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3_2.fastq.gz            --un-gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3/unmapped/single.fastq.gz            --un-conc-gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3/unmapped/pair.fastq.gz            -S out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.sam                        2> out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

        ln -srf out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3/unmapped/single.fastq.gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3/unmapped_single.fastq.gz
        ln -srf out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3/unmapped/pair.fastq.1.gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3/unmapped_pair1.fastq.gz
        ln -srf out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3/unmapped/pair.fastq.2.gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3/unmapped_pair2.fastq.gz
        

[Sat Apr 17 13:59:04 2021]
rule bowtie2_paired_end_extra:
    input: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3_2.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2
    output: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.sam, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3/unmapped/single.fastq.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3/unmapped/pair.fastq.1.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3/unmapped/pair.fastq.2.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3/unmapped_single.fastq.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3/unmapped_pair1.fastq.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3/unmapped_pair2.fastq.gz
    log: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 3356
    reason: Missing output files: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.sam; Input files updated by another job: out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3_2.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3_1.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2
    wildcards: tool=bowtie2/pe, extra=, index=hg19, filler=sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    threads: 2


        bowtie2 -p 2 -x out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome            -1 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3_1.fastq.gz -2 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3_2.fastq.gz            --un-gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3/unmapped/single.fastq.gz            --un-conc-gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3/unmapped/pair.fastq.gz            -S out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.sam                        2> out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

        ln -srf out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3/unmapped/single.fastq.gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3/unmapped_single.fastq.gz
        ln -srf out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3/unmapped/pair.fastq.1.gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3/unmapped_pair1.fastq.gz
        ln -srf out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3/unmapped/pair.fastq.2.gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3/unmapped_pair2.fastq.gz
        

[Sat Apr 17 13:59:04 2021]
rule sickle_se_extra:
    input: out/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.fastq.gz
    output: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.fastq.gz
    log: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.fastq.gz.log
    jobid: 3675
    reason: Missing output files: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.fastq.gz; Input files updated by another job: out/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.fastq.gz
    wildcards: tool=sickle/se, extra=_-t_sanger_-q_20, filler=ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3, ext=fastq.gz

sickle se -f out/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.fastq.gz  -t sanger -q 20 -g -o out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.fastq.gz &> out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.fastq.gz.log

[Sat Apr 17 13:59:04 2021]
rule bowtie2_paired_end_extra:
    input: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3_2.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2
    output: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.sam, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3/unmapped/single.fastq.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3/unmapped/pair.fastq.1.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3/unmapped/pair.fastq.2.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3/unmapped_single.fastq.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3/unmapped_pair1.fastq.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3/unmapped_pair2.fastq.gz
    log: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 3346
    reason: Missing output files: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.sam; Input files updated by another job: out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3_2.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3_1.fastq.gz
    wildcards: tool=bowtie2/pe, extra=, index=hg19, filler=sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    threads: 2


        bowtie2 -p 2 -x out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome            -1 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3_1.fastq.gz -2 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3_2.fastq.gz            --un-gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3/unmapped/single.fastq.gz            --un-conc-gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3/unmapped/pair.fastq.gz            -S out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.sam                        2> out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

        ln -srf out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3/unmapped/single.fastq.gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3/unmapped_single.fastq.gz
        ln -srf out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3/unmapped/pair.fastq.1.gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3/unmapped_pair1.fastq.gz
        ln -srf out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3/unmapped/pair.fastq.2.gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3/unmapped_pair2.fastq.gz
        

[Sat Apr 17 13:59:04 2021]
rule sickle_se_extra:
    input: out/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.fastq.gz
    output: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.fastq.gz
    log: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.fastq.gz.log
    jobid: 3573
    reason: Missing output files: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.fastq.gz; Input files updated by another job: out/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.fastq.gz
    wildcards: tool=sickle/se, extra=_-t_sanger_-q_20, filler=ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3, ext=fastq.gz

sickle se -f out/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.fastq.gz  -t sanger -q 20 -g -o out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.fastq.gz &> out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.fastq.gz.log

[Sat Apr 17 13:59:04 2021]
rule sickle_se_extra:
    input: out/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.fastq.gz
    output: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.fastq.gz
    log: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.fastq.gz.log
    jobid: 3676
    reason: Missing output files: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.fastq.gz; Input files updated by another job: out/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.fastq.gz
    wildcards: tool=sickle/se, extra=_-t_sanger_-q_20, filler=ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3, ext=fastq.gz

sickle se -f out/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.fastq.gz  -t sanger -q 20 -g -o out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.fastq.gz &> out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.fastq.gz.log

[Sat Apr 17 13:59:04 2021]
rule sickle_se_extra:
    input: out/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.fastq.gz
    output: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.fastq.gz
    log: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.fastq.gz.log
    jobid: 3681
    reason: Missing output files: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.fastq.gz; Input files updated by another job: out/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.fastq.gz
    wildcards: tool=sickle/se, extra=_-t_sanger_-q_20, filler=ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI, ext=fastq.gz

sickle se -f out/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.fastq.gz  -t sanger -q 20 -g -o out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.fastq.gz &> out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.fastq.gz.log

[Sat Apr 17 13:59:04 2021]
rule cat:
    input: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.1.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.2.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.3.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.4.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.5.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.6.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.7.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.8.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.9.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.10.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.11.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.12.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.13.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.14.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.15.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.16.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.17.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.18.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.19.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.20.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.21.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.22.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.X.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.Y.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.MT.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.nonchromosomal.fa
    output: out/cat/assembly_ensembl/GRCh37.fa
    jobid: 3472
    reason: Missing output files: out/cat/assembly_ensembl/GRCh37.fa; Input files updated by another job: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.4.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.5.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.15.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.12.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.7.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.21.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.X.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.6.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.14.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.3.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.nonchromosomal.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.16.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.2.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.17.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.20.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.22.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.18.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.1.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.11.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.8.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.19.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.10.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.13.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.MT.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.Y.fa, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.9.fa
    wildcards: cat_id=assembly_ensembl/GRCh37.fa

cat out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.1.fa out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.2.fa out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.3.fa out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.4.fa out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.5.fa out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.6.fa out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.7.fa out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.8.fa out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.9.fa out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.10.fa out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.11.fa out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.12.fa out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.13.fa out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.14.fa out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.15.fa out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.16.fa out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.17.fa out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.18.fa out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.19.fa out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.20.fa out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.21.fa out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.22.fa out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.X.fa out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.Y.fa out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.chromosome.MT.fa out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna.nonchromosomal.fa > out/cat/assembly_ensembl/GRCh37.fa

[Sat Apr 17 13:59:04 2021]
rule sickle_se_extra:
    input: out/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.fastq.gz
    output: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.fastq.gz
    log: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.fastq.gz.log
    jobid: 3572
    reason: Missing output files: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.fastq.gz; Input files updated by another job: out/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.fastq.gz
    wildcards: tool=sickle/se, extra=_-t_sanger_-q_20, filler=ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3, ext=fastq.gz

sickle se -f out/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.fastq.gz  -t sanger -q 20 -g -o out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.fastq.gz &> out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.fastq.gz.log

[Sat Apr 17 13:59:04 2021]
rule bowtie2_paired_end_extra:
    input: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3_2.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2
    output: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.sam, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3/unmapped/single.fastq.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3/unmapped/pair.fastq.1.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3/unmapped/pair.fastq.2.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3/unmapped_single.fastq.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3/unmapped_pair1.fastq.gz, out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3/unmapped_pair2.fastq.gz
    log: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 3340
    reason: Missing output files: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.sam; Input files updated by another job: out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3_2.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3_1.fastq.gz
    wildcards: tool=bowtie2/pe, extra=, index=hg19, filler=sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    threads: 2


        bowtie2 -p 2 -x out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome            -1 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3_1.fastq.gz -2 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3_2.fastq.gz            --un-gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3/unmapped/single.fastq.gz            --un-conc-gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3/unmapped/pair.fastq.gz            -S out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.sam                        2> out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

        ln -srf out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3/unmapped/single.fastq.gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3/unmapped_single.fastq.gz
        ln -srf out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3/unmapped/pair.fastq.1.gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3/unmapped_pair1.fastq.gz
        ln -srf out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3/unmapped/pair.fastq.2.gz out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3/unmapped_pair2.fastq.gz
        

[Sat Apr 17 13:59:04 2021]
rule gtftk_convert_ensembl:
    input: out/gunzip/to-stdout/wget/https/ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.gtf
    output: out/gtftk/convert_ensembl/gunzip/to-stdout/wget/https/ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.gtf
    jobid: 3336
    reason: Missing output files: out/gtftk/convert_ensembl/gunzip/to-stdout/wget/https/ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.gtf; Input files updated by another job: out/gunzip/to-stdout/wget/https/ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.gtf
    wildcards: filler=gunzip/to-stdout/wget/https/ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic

gtftk convert_ensembl --inputfile out/gunzip/to-stdout/wget/https/ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.gtf --outputfile out/gtftk/convert_ensembl/gunzip/to-stdout/wget/https/ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.gtf

[Sat Apr 17 13:59:04 2021]
rule sort_extra:
    input: out/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.BedGraph
    output: out/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.BedGraph
    jobid: 2209
    reason: Missing output files: out/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.BedGraph; Input files updated by another job: out/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.BedGraph
    wildcards: tool=sort/, extra=_-k1,1_-k2,2n, filler=tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.BedGraph

LC_ALL=C; sort  -k1,1 -k2,2n out/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.BedGraph > out/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.BedGraph

[Sat Apr 17 13:59:04 2021]
rule sickle_se_extra:
    input: out/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.fastq.gz
    output: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.fastq.gz
    log: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.fastq.gz.log
    jobid: 3682
    reason: Missing output files: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.fastq.gz; Input files updated by another job: out/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.fastq.gz
    wildcards: tool=sickle/se, extra=_-t_sanger_-q_20, filler=ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2, ext=fastq.gz

sickle se -f out/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.fastq.gz  -t sanger -q 20 -g -o out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.fastq.gz &> out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.fastq.gz.log

[Sat Apr 17 13:59:04 2021]
rule sickle_se_extra:
    input: out/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.fastq.gz
    output: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.fastq.gz
    log: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.fastq.gz.log
    jobid: 3674
    reason: Missing output files: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.fastq.gz; Input files updated by another job: out/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.fastq.gz
    wildcards: tool=sickle/se, extra=_-t_sanger_-q_20, filler=ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3, ext=fastq.gz

sickle se -f out/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.fastq.gz  -t sanger -q 20 -g -o out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.fastq.gz &> out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.fastq.gz.log

[Sat Apr 17 13:59:04 2021]
rule sickle_se_extra:
    input: out/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.fastq.gz
    output: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.fastq.gz
    log: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.fastq.gz.log
    jobid: 3680
    reason: Missing output files: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.fastq.gz; Input files updated by another job: out/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.fastq.gz
    wildcards: tool=sickle/se, extra=_-t_sanger_-q_20, filler=ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2, ext=fastq.gz

sickle se -f out/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.fastq.gz  -t sanger -q 20 -g -o out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.fastq.gz &> out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.fastq.gz.log

[Sat Apr 17 13:59:04 2021]
rule sickle_se_extra:
    input: out/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.fastq.gz
    output: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.fastq.gz
    log: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.fastq.gz.log
    jobid: 3506
    reason: Missing output files: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.fastq.gz; Input files updated by another job: out/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.fastq.gz
    wildcards: tool=sickle/se, extra=_-t_sanger_-q_20, filler=ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2, ext=fastq.gz

sickle se -f out/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.fastq.gz  -t sanger -q 20 -g -o out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.fastq.gz &> out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.fastq.gz.log

[Sat Apr 17 13:59:04 2021]
localrule ln_alias:
    input: out/cat/merge-fastq-samples/DND-41_SRX186659_H3K36me3.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.fastq.gz
    jobid: 3688
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.fastq.gz; Input files updated by another job: out/cat/merge-fastq-samples/DND-41_SRX186659_H3K36me3.fastq.gz
    wildcards: id=sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.fastq.gz
    priority: 10

ln -srf 'out/cat/merge-fastq-samples/DND-41_SRX186659_H3K36me3.fastq.gz' out/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.fastq.gz

[Sat Apr 17 13:59:04 2021]
localrule ln_alias:
    input: out/cat/merge-fastq-samples/Loucy_SRX2636361_H3K36me3.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.fastq.gz
    jobid: 3699
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.fastq.gz; Input files updated by another job: out/cat/merge-fastq-samples/Loucy_SRX2636361_H3K36me3.fastq.gz
    wildcards: id=sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.fastq.gz
    priority: 10

ln -srf 'out/cat/merge-fastq-samples/Loucy_SRX2636361_H3K36me3.fastq.gz' out/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.fastq.gz

[Sat Apr 17 13:59:04 2021]
localrule ln_alias:
    input: out/cat/merge-fastq-samples/DND-41_SRX186665_H3K79me2.fastq.gz
    output: out/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.fastq.gz
    jobid: 3689
    reason: Missing output files: out/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.fastq.gz; Input files updated by another job: out/cat/merge-fastq-samples/DND-41_SRX186665_H3K79me2.fastq.gz
    wildcards: id=sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.fastq.gz
    priority: 10

ln -srf 'out/cat/merge-fastq-samples/DND-41_SRX186665_H3K79me2.fastq.gz' out/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.fastq.gz

[Sat Apr 17 13:59:04 2021]
rule bowtie2_paired_end_extra:
    input: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3_2.fastq.gz, out/bowtie2-build/fa-genome-BDGP6.1.bt2, out/bowtie2-build/fa-genome-BDGP6.2.bt2, out/bowtie2-build/fa-genome-BDGP6.3.bt2, out/bowtie2-build/fa-genome-BDGP6.4.bt2, out/bowtie2-build/fa-genome-BDGP6.rev.1.bt2, out/bowtie2-build/fa-genome-BDGP6.rev.2.bt2
    output: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.sam, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3/unmapped/single.fastq.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3/unmapped/pair.fastq.1.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3/unmapped/pair.fastq.2.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3/unmapped_single.fastq.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3/unmapped_pair1.fastq.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3/unmapped_pair2.fastq.gz
    log: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 3353
    reason: Missing output files: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.sam; Input files updated by another job: out/bowtie2-build/fa-genome-BDGP6.rev.1.bt2, out/bowtie2-build/fa-genome-BDGP6.2.bt2, out/bowtie2-build/fa-genome-BDGP6.3.bt2, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3_1.fastq.gz, out/bowtie2-build/fa-genome-BDGP6.1.bt2, out/bowtie2-build/fa-genome-BDGP6.4.bt2, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3_2.fastq.gz, out/bowtie2-build/fa-genome-BDGP6.rev.2.bt2
    wildcards: tool=bowtie2/pe, extra=, index=BDGP6, filler=sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    threads: 2


        bowtie2 -p 2 -x out/bowtie2-build/fa-genome-BDGP6            -1 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3_1.fastq.gz -2 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3_2.fastq.gz            --un-gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3/unmapped/single.fastq.gz            --un-conc-gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3/unmapped/pair.fastq.gz            -S out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.sam                        2> out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

        ln -srf out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3/unmapped/single.fastq.gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3/unmapped_single.fastq.gz
        ln -srf out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3/unmapped/pair.fastq.1.gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3/unmapped_pair1.fastq.gz
        ln -srf out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3/unmapped/pair.fastq.2.gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3/unmapped_pair2.fastq.gz
        

[Sat Apr 17 13:59:04 2021]
rule samtools_sam_to_bam_bai_extra:
    input: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.sam
    output: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam.bai
    log: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 2367
    reason: Missing output files: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam; Input files updated by another job: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.sam
    wildcards: tool=samtools/sam_to_bam_bai, extra=_-q_30, filler=bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3


        (
        samtools view -bSh  -q 30 out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.sam | samtools sort -o out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam
        samtools index out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam
        ) &> out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
        

[Sat Apr 17 13:59:04 2021]
rule samtools_view_sam_to_bam_extra:
    input: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.sam
    output: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam
    log: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 3645
    reason: Missing output files: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam; Input files updated by another job: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.sam
    wildcards: tool=samtools/view_sam_to_bam, extra=_-q_30, filler=bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3

samtools view -bSh  -q 30 out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.sam -o out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam &> out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:04 2021]
rule sickle_pe_extra:
    input: out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM_1.fastq.gz, out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM_2.fastq.gz
    output: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM_2.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM_single.fastq.gz
    log: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM.fastq.gz.log
    jobid: 3415
    reason: Missing output files: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM_2.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM_1.fastq.gz; Input files updated by another job: out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM_1.fastq.gz, out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM_2.fastq.gz
    wildcards: tool=sickle/pe, extra=_-t_sanger_-q_20, filler=ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM, ext=fastq.gz

sickle pe -f out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM_1.fastq.gz -r out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM_2.fastq.gz -o out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM_1.fastq.gz -p out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM_2.fastq.gz -s out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM_single.fastq.gz  -t sanger -q 20 -g &> out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM.fastq.gz.log

[Sat Apr 17 13:59:04 2021]
rule samtools_view_sam_to_bam_extra:
    input: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.sam
    output: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam
    log: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 3647
    reason: Missing output files: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam; Input files updated by another job: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.sam
    wildcards: tool=samtools/view_sam_to_bam, extra=_-q_30, filler=bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3

samtools view -bSh  -q 30 out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.sam -o out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam &> out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:04 2021]
rule bowtie2_single_end_extra:
    input: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2
    output: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.sam, out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7_single.fastq.gz
    log: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.log
    jobid: 3661
    reason: Missing output files: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.sam; Input files updated by another job: out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2
    wildcards: tool=bowtie2/se, extra=, index=hg19, filler=sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7
    threads: 2


        bowtie2 -p 2 -x out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome             -U out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.fastq.gz             --un-gz out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7_single.fastq.gz             -S out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.sam                         2> out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.log
        

[Sat Apr 17 13:59:04 2021]
rule sickle_pe_extra:
    input: out/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h_1.fastq.gz, out/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h_2.fastq.gz
    output: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h_2.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h_single.fastq.gz
    log: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h.fastq.gz.log
    jobid: 3411
    reason: Missing output files: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h_2.fastq.gz; Input files updated by another job: out/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h_2.fastq.gz, out/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h_1.fastq.gz
    wildcards: tool=sickle/pe, extra=_-t_sanger_-q_20, filler=ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h, ext=fastq.gz

sickle pe -f out/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h_1.fastq.gz -r out/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h_2.fastq.gz -o out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h_1.fastq.gz -p out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h_2.fastq.gz -s out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h_single.fastq.gz  -t sanger -q 20 -g &> out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h.fastq.gz.log

[Sat Apr 17 13:59:04 2021]
rule bowtie2_single_end_extra:
    input: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2
    output: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.sam, out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3_single.fastq.gz
    log: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.log
    jobid: 3509
    reason: Missing output files: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.sam; Input files updated by another job: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2
    wildcards: tool=bowtie2/se, extra=, index=hg19, filler=sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3
    threads: 2


        bowtie2 -p 2 -x out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome             -U out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.fastq.gz             --un-gz out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3_single.fastq.gz             -S out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.sam                         2> out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.log
        

[Sat Apr 17 13:59:04 2021]
rule samtools_sam_to_bam_bai_extra:
    input: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.sam
    output: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam.bai
    log: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 2363
    reason: Missing output files: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam; Input files updated by another job: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.sam
    wildcards: tool=samtools/sam_to_bam_bai, extra=_-q_30, filler=bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3


        (
        samtools view -bSh  -q 30 out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.sam | samtools sort -o out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam
        samtools index out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam
        ) &> out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
        

[Sat Apr 17 13:59:04 2021]
rule samtools_view_sam_to_bam_extra:
    input: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.sam
    output: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam
    log: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 3654
    reason: Missing output files: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam; Input files updated by another job: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.sam
    wildcards: tool=samtools/view_sam_to_bam, extra=_-q_30, filler=bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3

samtools view -bSh  -q 30 out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.sam -o out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam &> out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:04 2021]
rule samtools_sam_to_bam_bai_extra:
    input: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.sam
    output: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam.bai
    log: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 2365
    reason: Missing output files: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam; Input files updated by another job: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.sam
    wildcards: tool=samtools/sam_to_bam_bai, extra=_-q_30, filler=bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3


        (
        samtools view -bSh  -q 30 out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.sam | samtools sort -o out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam
        samtools index out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam
        ) &> out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
        

[Sat Apr 17 13:59:04 2021]
rule samtools_sam_to_bam_bai_extra:
    input: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.sam
    output: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam.bai
    log: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2381
    reason: Missing output files: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam; Input files updated by another job: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.sam
    wildcards: tool=samtools/sam_to_bam_bai, extra=_-q_30, filler=bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3


        (
        samtools view -bSh  -q 30 out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.sam | samtools sort -o out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam
        samtools index out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam
        ) &> out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
        

[Sat Apr 17 13:59:04 2021]
rule gtftk_get_5p_3p_coords:
    input: out/gtftk/convert_ensembl/gunzip/to-stdout/wget/https/ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.gtf
    output: out/gtftk/get_5p_3p_coords/gtftk/convert_ensembl/gunzip/to-stdout/wget/https/ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.bed
    jobid: 2355
    reason: Missing output files: out/gtftk/get_5p_3p_coords/gtftk/convert_ensembl/gunzip/to-stdout/wget/https/ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.bed; Input files updated by another job: out/gtftk/convert_ensembl/gunzip/to-stdout/wget/https/ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.gtf
    wildcards: tool=gtftk/get_5p_3p_coords, extra=, filler=gtftk/convert_ensembl/gunzip/to-stdout/wget/https/ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic

['gene_id', 'transcript_id', 'gene_name']
gtftk get_5p_3p_coords  --inputfile out/gtftk/convert_ensembl/gunzip/to-stdout/wget/https/ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.gtf --outputfile out/gtftk/get_5p_3p_coords/gtftk/convert_ensembl/gunzip/to-stdout/wget/https/ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.bed

[Sat Apr 17 13:59:04 2021]
rule bowtie2_paired_end_extra:
    input: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3_2.fastq.gz, out/bowtie2-build/fa-genome-BDGP6.1.bt2, out/bowtie2-build/fa-genome-BDGP6.2.bt2, out/bowtie2-build/fa-genome-BDGP6.3.bt2, out/bowtie2-build/fa-genome-BDGP6.4.bt2, out/bowtie2-build/fa-genome-BDGP6.rev.1.bt2, out/bowtie2-build/fa-genome-BDGP6.rev.2.bt2
    output: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.sam, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3/unmapped/single.fastq.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3/unmapped/pair.fastq.1.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3/unmapped/pair.fastq.2.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3/unmapped_single.fastq.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3/unmapped_pair1.fastq.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3/unmapped_pair2.fastq.gz
    log: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 3355
    reason: Missing output files: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.sam; Input files updated by another job: out/bowtie2-build/fa-genome-BDGP6.rev.1.bt2, out/bowtie2-build/fa-genome-BDGP6.2.bt2, out/bowtie2-build/fa-genome-BDGP6.3.bt2, out/bowtie2-build/fa-genome-BDGP6.1.bt2, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3_1.fastq.gz, out/bowtie2-build/fa-genome-BDGP6.4.bt2, out/bowtie2-build/fa-genome-BDGP6.rev.2.bt2, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3_2.fastq.gz
    wildcards: tool=bowtie2/pe, extra=, index=BDGP6, filler=sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    threads: 2


        bowtie2 -p 2 -x out/bowtie2-build/fa-genome-BDGP6            -1 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3_1.fastq.gz -2 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3_2.fastq.gz            --un-gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3/unmapped/single.fastq.gz            --un-conc-gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3/unmapped/pair.fastq.gz            -S out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.sam                        2> out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

        ln -srf out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3/unmapped/single.fastq.gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3/unmapped_single.fastq.gz
        ln -srf out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3/unmapped/pair.fastq.1.gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3/unmapped_pair1.fastq.gz
        ln -srf out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3/unmapped/pair.fastq.2.gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3/unmapped_pair2.fastq.gz
        

[Sat Apr 17 13:59:04 2021]
rule samtools_view_sam_to_bam_extra:
    input: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.sam
    output: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam
    log: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 3646
    reason: Missing output files: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam; Input files updated by another job: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.sam
    wildcards: tool=samtools/view_sam_to_bam, extra=_-q_30, filler=bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3

samtools view -bSh  -q 30 out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.sam -o out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam &> out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:04 2021]
rule bowtie2_paired_end_extra:
    input: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3_2.fastq.gz, out/bowtie2-build/fa-genome-BDGP6.1.bt2, out/bowtie2-build/fa-genome-BDGP6.2.bt2, out/bowtie2-build/fa-genome-BDGP6.3.bt2, out/bowtie2-build/fa-genome-BDGP6.4.bt2, out/bowtie2-build/fa-genome-BDGP6.rev.1.bt2, out/bowtie2-build/fa-genome-BDGP6.rev.2.bt2
    output: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.sam, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3/unmapped/single.fastq.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3/unmapped/pair.fastq.1.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3/unmapped/pair.fastq.2.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3/unmapped_single.fastq.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3/unmapped_pair1.fastq.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3/unmapped_pair2.fastq.gz
    log: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 3359
    reason: Missing output files: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.sam; Input files updated by another job: out/bowtie2-build/fa-genome-BDGP6.rev.1.bt2, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3_1.fastq.gz, out/bowtie2-build/fa-genome-BDGP6.2.bt2, out/bowtie2-build/fa-genome-BDGP6.3.bt2, out/bowtie2-build/fa-genome-BDGP6.1.bt2, out/bowtie2-build/fa-genome-BDGP6.4.bt2, out/bowtie2-build/fa-genome-BDGP6.rev.2.bt2, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3_2.fastq.gz
    wildcards: tool=bowtie2/pe, extra=, index=BDGP6, filler=sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    threads: 2


        bowtie2 -p 2 -x out/bowtie2-build/fa-genome-BDGP6            -1 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3_1.fastq.gz -2 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3_2.fastq.gz            --un-gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3/unmapped/single.fastq.gz            --un-conc-gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3/unmapped/pair.fastq.gz            -S out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.sam                        2> out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

        ln -srf out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3/unmapped/single.fastq.gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3/unmapped_single.fastq.gz
        ln -srf out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3/unmapped/pair.fastq.1.gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3/unmapped_pair1.fastq.gz
        ln -srf out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3/unmapped/pair.fastq.2.gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3/unmapped_pair2.fastq.gz
        

[Sat Apr 17 13:59:04 2021]
rule sickle_se_extra:
    input: out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM.fastq.gz
    output: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM.fastq.gz
    log: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM.fastq.gz.log
    jobid: 3418
    reason: Missing output files: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM.fastq.gz; Input files updated by another job: out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM.fastq.gz
    wildcards: tool=sickle/se, extra=_-t_sanger_-q_20, filler=ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM, ext=fastq.gz

sickle se -f out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM.fastq.gz  -t sanger -q 20 -g -o out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM.fastq.gz &> out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM.fastq.gz.log

[Sat Apr 17 13:59:04 2021]
rule ucsc_bedGraphToBigWig:
    input: out/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.BedGraph, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt
    output: out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.bw
    jobid: 38
    reason: Missing output files: out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.bw; Input files updated by another job: out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.BedGraph
    wildcards: chrominfo_id=chrominfo-hg19, filler=sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph


        bedGraphToBigWig out/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.BedGraph out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.bw
        

[Sat Apr 17 13:59:04 2021]
rule bowtie2_single_end_extra:
    input: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2
    output: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.sam, out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3_single.fastq.gz
    log: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 3658
    reason: Missing output files: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.sam; Input files updated by another job: out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2
    wildcards: tool=bowtie2/se, extra=, index=hg19, filler=sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3
    threads: 2


        bowtie2 -p 2 -x out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome             -U out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.fastq.gz             --un-gz out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3_single.fastq.gz             -S out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.sam                         2> out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.log
        

[Sat Apr 17 13:59:04 2021]
rule samtools_sam_to_bam_bai_extra:
    input: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.sam
    output: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam.bai
    log: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2373
    reason: Missing output files: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam; Input files updated by another job: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.sam
    wildcards: tool=samtools/sam_to_bam_bai, extra=_-q_30, filler=bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3


        (
        samtools view -bSh  -q 30 out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.sam | samtools sort -o out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam
        samtools index out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam
        ) &> out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
        

[Sat Apr 17 13:59:04 2021]
rule sickle_pe_extra:
    input: out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM_1.fastq.gz, out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM_2.fastq.gz
    output: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM_2.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM_single.fastq.gz
    log: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM.fastq.gz.log
    jobid: 3417
    reason: Missing output files: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM_2.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM_1.fastq.gz; Input files updated by another job: out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM_2.fastq.gz, out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM_1.fastq.gz
    wildcards: tool=sickle/pe, extra=_-t_sanger_-q_20, filler=ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM, ext=fastq.gz

sickle pe -f out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM_1.fastq.gz -r out/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM_2.fastq.gz -o out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM_1.fastq.gz -p out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM_2.fastq.gz -s out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM_single.fastq.gz  -t sanger -q 20 -g &> out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM.fastq.gz.log

[Sat Apr 17 13:59:04 2021]
rule sickle_pe_extra:
    input: out/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h_1.fastq.gz, out/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h_2.fastq.gz
    output: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h_2.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h_single.fastq.gz
    log: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h.fastq.gz.log
    jobid: 3416
    reason: Missing output files: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h_2.fastq.gz; Input files updated by another job: out/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h_2.fastq.gz, out/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h_1.fastq.gz
    wildcards: tool=sickle/pe, extra=_-t_sanger_-q_20, filler=ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h, ext=fastq.gz

sickle pe -f out/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h_1.fastq.gz -r out/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h_2.fastq.gz -o out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h_1.fastq.gz -p out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h_2.fastq.gz -s out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h_single.fastq.gz  -t sanger -q 20 -g &> out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h.fastq.gz.log

[Sat Apr 17 13:59:04 2021]
rule bowtie2_single_end_extra:
    input: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2
    output: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.sam, out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3_single.fastq.gz
    log: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.log
    jobid: 3508
    reason: Missing output files: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.sam; Input files updated by another job: out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.fastq.gz
    wildcards: tool=bowtie2/se, extra=, index=hg19, filler=sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3
    threads: 2


        bowtie2 -p 2 -x out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome             -U out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.fastq.gz             --un-gz out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3_single.fastq.gz             -S out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.sam                         2> out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.log
        

[Sat Apr 17 13:59:04 2021]
rule sickle_pe_extra:
    input: out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM_1.fastq.gz, out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM_2.fastq.gz
    output: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM_2.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM_single.fastq.gz
    log: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM.fastq.gz.log
    jobid: 3414
    reason: Missing output files: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM_2.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM_1.fastq.gz; Input files updated by another job: out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM_1.fastq.gz, out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM_2.fastq.gz
    wildcards: tool=sickle/pe, extra=_-t_sanger_-q_20, filler=ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM, ext=fastq.gz

sickle pe -f out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM_1.fastq.gz -r out/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM_2.fastq.gz -o out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM_1.fastq.gz -p out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM_2.fastq.gz -s out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM_single.fastq.gz  -t sanger -q 20 -g &> out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM.fastq.gz.log

[Sat Apr 17 13:59:04 2021]
rule samtools_view_sam_to_bam_extra:
    input: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.sam
    output: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam
    log: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 3650
    reason: Missing output files: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam; Input files updated by another job: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.sam
    wildcards: tool=samtools/view_sam_to_bam, extra=_-q_30, filler=bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3

samtools view -bSh  -q 30 out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.sam -o out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam &> out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:04 2021]
rule bowtie2_paired_end_extra:
    input: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3_2.fastq.gz, out/bowtie2-build/fa-genome-BDGP6.1.bt2, out/bowtie2-build/fa-genome-BDGP6.2.bt2, out/bowtie2-build/fa-genome-BDGP6.3.bt2, out/bowtie2-build/fa-genome-BDGP6.4.bt2, out/bowtie2-build/fa-genome-BDGP6.rev.1.bt2, out/bowtie2-build/fa-genome-BDGP6.rev.2.bt2
    output: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.sam, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3/unmapped/single.fastq.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3/unmapped/pair.fastq.1.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3/unmapped/pair.fastq.2.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3/unmapped_single.fastq.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3/unmapped_pair1.fastq.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3/unmapped_pair2.fastq.gz
    log: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 3341
    reason: Missing output files: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.sam; Input files updated by another job: out/bowtie2-build/fa-genome-BDGP6.rev.1.bt2, out/bowtie2-build/fa-genome-BDGP6.2.bt2, out/bowtie2-build/fa-genome-BDGP6.3.bt2, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3_2.fastq.gz, out/bowtie2-build/fa-genome-BDGP6.1.bt2, out/bowtie2-build/fa-genome-BDGP6.4.bt2, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3_1.fastq.gz, out/bowtie2-build/fa-genome-BDGP6.rev.2.bt2
    wildcards: tool=bowtie2/pe, extra=, index=BDGP6, filler=sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    threads: 2


        bowtie2 -p 2 -x out/bowtie2-build/fa-genome-BDGP6            -1 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3_1.fastq.gz -2 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3_2.fastq.gz            --un-gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3/unmapped/single.fastq.gz            --un-conc-gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3/unmapped/pair.fastq.gz            -S out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.sam                        2> out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

        ln -srf out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3/unmapped/single.fastq.gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3/unmapped_single.fastq.gz
        ln -srf out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3/unmapped/pair.fastq.1.gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3/unmapped_pair1.fastq.gz
        ln -srf out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3/unmapped/pair.fastq.2.gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3/unmapped_pair2.fastq.gz
        

[Sat Apr 17 13:59:04 2021]
rule bowtie2_single_end_extra:
    input: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2
    output: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.sam, out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2_single.fastq.gz
    log: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.log
    jobid: 3443
    reason: Missing output files: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.sam; Input files updated by another job: out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2
    wildcards: tool=bowtie2/se, extra=, index=hg19, filler=sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2
    threads: 2


        bowtie2 -p 2 -x out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome             -U out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.fastq.gz             --un-gz out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2_single.fastq.gz             -S out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.sam                         2> out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.log
        

[Sat Apr 17 13:59:04 2021]
rule bowtie2_single_end_extra:
    input: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2
    output: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.sam, out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3_single.fastq.gz
    log: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 3660
    reason: Missing output files: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.sam; Input files updated by another job: out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2
    wildcards: tool=bowtie2/se, extra=, index=hg19, filler=sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3
    threads: 2


        bowtie2 -p 2 -x out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome             -U out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.fastq.gz             --un-gz out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3_single.fastq.gz             -S out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.sam                         2> out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.log
        

[Sat Apr 17 13:59:04 2021]
rule bowtie2_single_end_extra:
    input: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2
    output: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.sam, out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3_single.fastq.gz
    log: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 3657
    reason: Missing output files: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.sam; Input files updated by another job: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2
    wildcards: tool=bowtie2/se, extra=, index=hg19, filler=sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3
    threads: 2


        bowtie2 -p 2 -x out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome             -U out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.fastq.gz             --un-gz out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3_single.fastq.gz             -S out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.sam                         2> out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.log
        

[Sat Apr 17 13:59:04 2021]
rule ucsc_bedGraphToBigWig:
    input: out/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.BedGraph, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt
    output: out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.bw
    jobid: 40
    reason: Missing output files: out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.bw; Input files updated by another job: out/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.BedGraph, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt
    wildcards: chrominfo_id=chrominfo-hg19, filler=sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph


        bedGraphToBigWig out/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.BedGraph out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.bw
        

[Sat Apr 17 13:59:04 2021]
rule bowtie2_single_end_extra:
    input: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2
    output: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.sam, out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3_single.fastq.gz
    log: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.log
    jobid: 3662
    reason: Missing output files: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.sam; Input files updated by another job: out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2, out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2
    wildcards: tool=bowtie2/se, extra=, index=hg19, filler=sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3
    threads: 2


        bowtie2 -p 2 -x out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome             -U out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.fastq.gz             --un-gz out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3_single.fastq.gz             -S out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.sam                         2> out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.log
        

[Sat Apr 17 13:59:04 2021]
rule bowtie2_single_end_extra:
    input: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2
    output: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.sam, out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2_single.fastq.gz
    log: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.log
    jobid: 3663
    reason: Missing output files: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.sam; Input files updated by another job: out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2
    wildcards: tool=bowtie2/se, extra=, index=hg19, filler=sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2
    threads: 2


        bowtie2 -p 2 -x out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome             -U out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.fastq.gz             --un-gz out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2_single.fastq.gz             -S out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.sam                         2> out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.log
        

[Sat Apr 17 13:59:04 2021]
rule bowtie2_paired_end_extra:
    input: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3_2.fastq.gz, out/bowtie2-build/fa-genome-BDGP6.1.bt2, out/bowtie2-build/fa-genome-BDGP6.2.bt2, out/bowtie2-build/fa-genome-BDGP6.3.bt2, out/bowtie2-build/fa-genome-BDGP6.4.bt2, out/bowtie2-build/fa-genome-BDGP6.rev.1.bt2, out/bowtie2-build/fa-genome-BDGP6.rev.2.bt2
    output: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.sam, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3/unmapped/single.fastq.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3/unmapped/pair.fastq.1.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3/unmapped/pair.fastq.2.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3/unmapped_single.fastq.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3/unmapped_pair1.fastq.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3/unmapped_pair2.fastq.gz
    log: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 3345
    reason: Missing output files: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.sam; Input files updated by another job: out/bowtie2-build/fa-genome-BDGP6.rev.1.bt2, out/bowtie2-build/fa-genome-BDGP6.2.bt2, out/bowtie2-build/fa-genome-BDGP6.4.bt2, out/bowtie2-build/fa-genome-BDGP6.3.bt2, out/bowtie2-build/fa-genome-BDGP6.1.bt2, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3_2.fastq.gz, out/bowtie2-build/fa-genome-BDGP6.rev.2.bt2
    wildcards: tool=bowtie2/pe, extra=, index=BDGP6, filler=sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    threads: 2


        bowtie2 -p 2 -x out/bowtie2-build/fa-genome-BDGP6            -1 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3_1.fastq.gz -2 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3_2.fastq.gz            --un-gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3/unmapped/single.fastq.gz            --un-conc-gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3/unmapped/pair.fastq.gz            -S out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.sam                        2> out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

        ln -srf out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3/unmapped/single.fastq.gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3/unmapped_single.fastq.gz
        ln -srf out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3/unmapped/pair.fastq.1.gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3/unmapped_pair1.fastq.gz
        ln -srf out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3/unmapped/pair.fastq.2.gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3/unmapped_pair2.fastq.gz
        

[Sat Apr 17 13:59:04 2021]
rule bowtie2_single_end_extra:
    input: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2
    output: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.sam, out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI_single.fastq.gz
    log: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.log
    jobid: 3664
    reason: Missing output files: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.sam; Input files updated by another job: out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2
    wildcards: tool=bowtie2/se, extra=, index=hg19, filler=sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI
    threads: 2


        bowtie2 -p 2 -x out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome             -U out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.fastq.gz             --un-gz out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI_single.fastq.gz             -S out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.sam                         2> out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.log
        

[Sat Apr 17 13:59:04 2021]
rule bowtie2_single_end_extra:
    input: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2
    output: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.sam, out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3_single.fastq.gz
    log: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.log
    jobid: 3505
    reason: Missing output files: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.sam; Input files updated by another job: out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.fastq.gz
    wildcards: tool=bowtie2/se, extra=, index=hg19, filler=sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3
    threads: 2


        bowtie2 -p 2 -x out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome             -U out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.fastq.gz             --un-gz out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3_single.fastq.gz             -S out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.sam                         2> out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.log
        

[Sat Apr 17 13:59:04 2021]
rule bowtie2_single_end_extra:
    input: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2
    output: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.sam, out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2_single.fastq.gz
    log: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.log
    jobid: 3665
    reason: Missing output files: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.sam; Input files updated by another job: out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.fastq.gz
    wildcards: tool=bowtie2/se, extra=, index=hg19, filler=sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2
    threads: 2


        bowtie2 -p 2 -x out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome             -U out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.fastq.gz             --un-gz out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2_single.fastq.gz             -S out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.sam                         2> out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.log
        

[Sat Apr 17 13:59:04 2021]
rule bowtie2_paired_end_extra:
    input: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3_2.fastq.gz, out/bowtie2-build/fa-genome-BDGP6.1.bt2, out/bowtie2-build/fa-genome-BDGP6.2.bt2, out/bowtie2-build/fa-genome-BDGP6.3.bt2, out/bowtie2-build/fa-genome-BDGP6.4.bt2, out/bowtie2-build/fa-genome-BDGP6.rev.1.bt2, out/bowtie2-build/fa-genome-BDGP6.rev.2.bt2
    output: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.sam, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3/unmapped/single.fastq.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3/unmapped/pair.fastq.1.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3/unmapped/pair.fastq.2.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3/unmapped_single.fastq.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3/unmapped_pair1.fastq.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3/unmapped_pair2.fastq.gz
    log: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 3349
    reason: Missing output files: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.sam; Input files updated by another job: out/bowtie2-build/fa-genome-BDGP6.rev.1.bt2, out/bowtie2-build/fa-genome-BDGP6.2.bt2, out/bowtie2-build/fa-genome-BDGP6.3.bt2, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3_2.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3_1.fastq.gz, out/bowtie2-build/fa-genome-BDGP6.1.bt2, out/bowtie2-build/fa-genome-BDGP6.4.bt2, out/bowtie2-build/fa-genome-BDGP6.rev.2.bt2
    wildcards: tool=bowtie2/pe, extra=, index=BDGP6, filler=sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    threads: 2


        bowtie2 -p 2 -x out/bowtie2-build/fa-genome-BDGP6            -1 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3_1.fastq.gz -2 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3_2.fastq.gz            --un-gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3/unmapped/single.fastq.gz            --un-conc-gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3/unmapped/pair.fastq.gz            -S out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.sam                        2> out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

        ln -srf out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3/unmapped/single.fastq.gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3/unmapped_single.fastq.gz
        ln -srf out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3/unmapped/pair.fastq.1.gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3/unmapped_pair1.fastq.gz
        ln -srf out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3/unmapped/pair.fastq.2.gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3/unmapped_pair2.fastq.gz
        

[Sat Apr 17 13:59:04 2021]
rule bowtie2_paired_end_extra:
    input: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3_2.fastq.gz, out/bowtie2-build/fa-genome-BDGP6.1.bt2, out/bowtie2-build/fa-genome-BDGP6.2.bt2, out/bowtie2-build/fa-genome-BDGP6.3.bt2, out/bowtie2-build/fa-genome-BDGP6.4.bt2, out/bowtie2-build/fa-genome-BDGP6.rev.1.bt2, out/bowtie2-build/fa-genome-BDGP6.rev.2.bt2
    output: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.sam, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3/unmapped/single.fastq.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3/unmapped/pair.fastq.1.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3/unmapped/pair.fastq.2.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3/unmapped_single.fastq.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3/unmapped_pair1.fastq.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3/unmapped_pair2.fastq.gz
    log: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 3347
    reason: Missing output files: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.sam; Input files updated by another job: out/bowtie2-build/fa-genome-BDGP6.rev.1.bt2, out/bowtie2-build/fa-genome-BDGP6.2.bt2, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3_2.fastq.gz, out/bowtie2-build/fa-genome-BDGP6.3.bt2, out/bowtie2-build/fa-genome-BDGP6.1.bt2, out/bowtie2-build/fa-genome-BDGP6.4.bt2, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3_1.fastq.gz, out/bowtie2-build/fa-genome-BDGP6.rev.2.bt2
    wildcards: tool=bowtie2/pe, extra=, index=BDGP6, filler=sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    threads: 2


        bowtie2 -p 2 -x out/bowtie2-build/fa-genome-BDGP6            -1 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3_1.fastq.gz -2 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3_2.fastq.gz            --un-gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3/unmapped/single.fastq.gz            --un-conc-gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3/unmapped/pair.fastq.gz            -S out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.sam                        2> out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

        ln -srf out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3/unmapped/single.fastq.gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3/unmapped_single.fastq.gz
        ln -srf out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3/unmapped/pair.fastq.1.gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3/unmapped_pair1.fastq.gz
        ln -srf out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3/unmapped/pair.fastq.2.gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3/unmapped_pair2.fastq.gz
        

[Sat Apr 17 13:59:04 2021]
rule bowtie2_single_end_extra:
    input: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2
    output: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.sam, out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3_single.fastq.gz
    log: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 3659
    reason: Missing output files: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.sam; Input files updated by another job: out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2, out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2
    wildcards: tool=bowtie2/se, extra=, index=hg19, filler=sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3
    threads: 2


        bowtie2 -p 2 -x out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome             -U out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.fastq.gz             --un-gz out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3_single.fastq.gz             -S out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.sam                         2> out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.log
        

[Sat Apr 17 13:59:04 2021]
rule samtools_view_sam_to_bam_extra:
    input: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.sam
    output: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam
    log: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 3652
    reason: Missing output files: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam; Input files updated by another job: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.sam
    wildcards: tool=samtools/view_sam_to_bam, extra=_-q_30, filler=bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3

samtools view -bSh  -q 30 out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.sam -o out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam &> out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:04 2021]
rule samtools_view_sam_to_bam_extra:
    input: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.sam
    output: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam
    log: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 3653
    reason: Missing output files: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam; Input files updated by another job: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.sam
    wildcards: tool=samtools/view_sam_to_bam, extra=_-q_30, filler=bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3

samtools view -bSh  -q 30 out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.sam -o out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam &> out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:04 2021]
rule samtools_view_sam_to_bam_extra:
    input: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.sam
    output: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam
    log: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 3651
    reason: Missing output files: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam; Input files updated by another job: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.sam
    wildcards: tool=samtools/view_sam_to_bam, extra=_-q_30, filler=bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3

samtools view -bSh  -q 30 out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.sam -o out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam &> out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:04 2021]
rule samtools_sam_to_bam_bai_extra:
    input: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.sam
    output: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam.bai
    log: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 2369
    reason: Missing output files: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam; Input files updated by another job: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.sam
    wildcards: tool=samtools/sam_to_bam_bai, extra=_-q_30, filler=bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3


        (
        samtools view -bSh  -q 30 out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.sam | samtools sort -o out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam
        samtools index out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam
        ) &> out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
        

[Sat Apr 17 13:59:04 2021]
rule samtools_sam_to_bam_bai_extra:
    input: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.sam
    output: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam.bai
    log: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2379
    reason: Missing output files: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam; Input files updated by another job: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.sam
    wildcards: tool=samtools/sam_to_bam_bai, extra=_-q_30, filler=bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3


        (
        samtools view -bSh  -q 30 out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.sam | samtools sort -o out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam
        samtools index out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam
        ) &> out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
        

[Sat Apr 17 13:59:04 2021]
rule samtools_sam_to_bam_bai_extra:
    input: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.sam
    output: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam.bai
    log: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2377
    reason: Missing output files: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam; Input files updated by another job: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.sam
    wildcards: tool=samtools/sam_to_bam_bai, extra=_-q_30, filler=bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3


        (
        samtools view -bSh  -q 30 out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.sam | samtools sort -o out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam
        samtools index out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam
        ) &> out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
        

[Sat Apr 17 13:59:04 2021]
rule bowtie2_paired_end_extra:
    input: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3_2.fastq.gz, out/bowtie2-build/fa-genome-BDGP6.1.bt2, out/bowtie2-build/fa-genome-BDGP6.2.bt2, out/bowtie2-build/fa-genome-BDGP6.3.bt2, out/bowtie2-build/fa-genome-BDGP6.4.bt2, out/bowtie2-build/fa-genome-BDGP6.rev.1.bt2, out/bowtie2-build/fa-genome-BDGP6.rev.2.bt2
    output: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.sam, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3/unmapped/single.fastq.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3/unmapped/pair.fastq.1.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3/unmapped/pair.fastq.2.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3/unmapped_single.fastq.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3/unmapped_pair1.fastq.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3/unmapped_pair2.fastq.gz
    log: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 3343
    reason: Missing output files: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.sam; Input files updated by another job: out/bowtie2-build/fa-genome-BDGP6.rev.1.bt2, out/bowtie2-build/fa-genome-BDGP6.2.bt2, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3_1.fastq.gz, out/bowtie2-build/fa-genome-BDGP6.3.bt2, out/bowtie2-build/fa-genome-BDGP6.1.bt2, out/bowtie2-build/fa-genome-BDGP6.rev.2.bt2, out/bowtie2-build/fa-genome-BDGP6.4.bt2, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3_2.fastq.gz
    wildcards: tool=bowtie2/pe, extra=, index=BDGP6, filler=sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    threads: 2


        bowtie2 -p 2 -x out/bowtie2-build/fa-genome-BDGP6            -1 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3_1.fastq.gz -2 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3_2.fastq.gz            --un-gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3/unmapped/single.fastq.gz            --un-conc-gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3/unmapped/pair.fastq.gz            -S out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.sam                        2> out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

        ln -srf out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3/unmapped/single.fastq.gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3/unmapped_single.fastq.gz
        ln -srf out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3/unmapped/pair.fastq.1.gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3/unmapped_pair1.fastq.gz
        ln -srf out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3/unmapped/pair.fastq.2.gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3/unmapped_pair2.fastq.gz
        

[Sat Apr 17 13:59:04 2021]
rule samtools_sam_to_bam_bai_extra:
    input: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.sam
    output: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam.bai
    log: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2375
    reason: Missing output files: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam; Input files updated by another job: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.sam
    wildcards: tool=samtools/sam_to_bam_bai, extra=_-q_30, filler=bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3


        (
        samtools view -bSh  -q 30 out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.sam | samtools sort -o out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam
        samtools index out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam
        ) &> out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
        

[Sat Apr 17 13:59:04 2021]
rule samtools_view_sam_to_bam_extra:
    input: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.sam
    output: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam
    log: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 3648
    reason: Missing output files: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam; Input files updated by another job: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.sam
    wildcards: tool=samtools/view_sam_to_bam, extra=_-q_30, filler=bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3

samtools view -bSh  -q 30 out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.sam -o out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam &> out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:04 2021]
rule bowtie2_paired_end_extra:
    input: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3_2.fastq.gz, out/bowtie2-build/fa-genome-BDGP6.1.bt2, out/bowtie2-build/fa-genome-BDGP6.2.bt2, out/bowtie2-build/fa-genome-BDGP6.3.bt2, out/bowtie2-build/fa-genome-BDGP6.4.bt2, out/bowtie2-build/fa-genome-BDGP6.rev.1.bt2, out/bowtie2-build/fa-genome-BDGP6.rev.2.bt2
    output: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.sam, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3/unmapped/single.fastq.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3/unmapped/pair.fastq.1.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3/unmapped/pair.fastq.2.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3/unmapped_single.fastq.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3/unmapped_pair1.fastq.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3/unmapped_pair2.fastq.gz
    log: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 3357
    reason: Missing output files: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.sam; Input files updated by another job: out/bowtie2-build/fa-genome-BDGP6.rev.1.bt2, out/bowtie2-build/fa-genome-BDGP6.2.bt2, out/bowtie2-build/fa-genome-BDGP6.3.bt2, out/bowtie2-build/fa-genome-BDGP6.1.bt2, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3_2.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3_1.fastq.gz, out/bowtie2-build/fa-genome-BDGP6.4.bt2, out/bowtie2-build/fa-genome-BDGP6.rev.2.bt2
    wildcards: tool=bowtie2/pe, extra=, index=BDGP6, filler=sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    threads: 2


        bowtie2 -p 2 -x out/bowtie2-build/fa-genome-BDGP6            -1 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3_1.fastq.gz -2 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3_2.fastq.gz            --un-gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3/unmapped/single.fastq.gz            --un-conc-gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3/unmapped/pair.fastq.gz            -S out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.sam                        2> out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

        ln -srf out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3/unmapped/single.fastq.gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3/unmapped_single.fastq.gz
        ln -srf out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3/unmapped/pair.fastq.1.gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3/unmapped_pair1.fastq.gz
        ln -srf out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3/unmapped/pair.fastq.2.gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3/unmapped_pair2.fastq.gz
        

[Sat Apr 17 13:59:04 2021]
rule bowtie2_paired_end_extra:
    input: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3_2.fastq.gz, out/bowtie2-build/fa-genome-BDGP6.1.bt2, out/bowtie2-build/fa-genome-BDGP6.2.bt2, out/bowtie2-build/fa-genome-BDGP6.3.bt2, out/bowtie2-build/fa-genome-BDGP6.4.bt2, out/bowtie2-build/fa-genome-BDGP6.rev.1.bt2, out/bowtie2-build/fa-genome-BDGP6.rev.2.bt2
    output: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.sam, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3/unmapped/single.fastq.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3/unmapped/pair.fastq.1.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3/unmapped/pair.fastq.2.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3/unmapped_single.fastq.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3/unmapped_pair1.fastq.gz, out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3/unmapped_pair2.fastq.gz
    log: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 3351
    reason: Missing output files: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.sam; Input files updated by another job: out/bowtie2-build/fa-genome-BDGP6.rev.1.bt2, out/bowtie2-build/fa-genome-BDGP6.2.bt2, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3_2.fastq.gz, out/bowtie2-build/fa-genome-BDGP6.3.bt2, out/bowtie2-build/fa-genome-BDGP6.1.bt2, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3_1.fastq.gz, out/bowtie2-build/fa-genome-BDGP6.4.bt2, out/bowtie2-build/fa-genome-BDGP6.rev.2.bt2
    wildcards: tool=bowtie2/pe, extra=, index=BDGP6, filler=sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    threads: 2


        bowtie2 -p 2 -x out/bowtie2-build/fa-genome-BDGP6            -1 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3_1.fastq.gz -2 out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3_2.fastq.gz            --un-gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3/unmapped/single.fastq.gz            --un-conc-gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3/unmapped/pair.fastq.gz            -S out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.sam                        2> out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

        ln -srf out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3/unmapped/single.fastq.gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3/unmapped_single.fastq.gz
        ln -srf out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3/unmapped/pair.fastq.1.gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3/unmapped_pair1.fastq.gz
        ln -srf out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3/unmapped/pair.fastq.2.gz out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3/unmapped_pair2.fastq.gz
        

[Sat Apr 17 13:59:04 2021]
rule samtools_view_sam_to_bam_extra:
    input: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.sam
    output: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam
    log: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 3649
    reason: Missing output files: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam; Input files updated by another job: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.sam
    wildcards: tool=samtools/view_sam_to_bam, extra=_-q_30, filler=bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3

samtools view -bSh  -q 30 out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.sam -o out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam &> out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:04 2021]
rule ucsc_bedGraphToBigWig:
    input: out/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.BedGraph, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt
    output: out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.bw
    jobid: 39
    reason: Missing output files: out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.bw; Input files updated by another job: out/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.BedGraph, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt
    wildcards: chrominfo_id=chrominfo-hg19, filler=sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph


        bedGraphToBigWig out/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.BedGraph out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.bw
        

[Sat Apr 17 13:59:04 2021]
rule bowtie2_single_end_extra:
    input: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2
    output: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.sam, out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3_single.fastq.gz
    log: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.log
    jobid: 3507
    reason: Missing output files: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.sam; Input files updated by another job: out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2
    wildcards: tool=bowtie2/se, extra=, index=hg19, filler=sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3
    threads: 2


        bowtie2 -p 2 -x out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome             -U out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.fastq.gz             --un-gz out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3_single.fastq.gz             -S out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.sam                         2> out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.log
        

[Sat Apr 17 13:59:04 2021]
rule star_build_index:
    input: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf, out/cat/assembly_ensembl/GRCh37.fa
    output: out/star/build_index/fa-genome-GRCh37_gtf-GRCh37-ensembl/genomeParameters.txt, out/star/build_index/fa-genome-GRCh37_gtf-GRCh37-ensembl/Genome
    jobid: 3412
    reason: Missing output files: out/star/build_index/fa-genome-GRCh37_gtf-GRCh37-ensembl/Genome; Input files updated by another job: out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf, out/cat/assembly_ensembl/GRCh37.fa
    wildcards: fa_id=fa-genome-GRCh37, gtf_id=gtf-GRCh37-ensembl
    threads: 2


        rm -rf out/star/build_index/fa-genome-GRCh37_gtf-GRCh37-ensembl/tmp

        STAR             --runThreadN 2             --runMode genomeGenerate             --genomeDir out/star/build_index/fa-genome-GRCh37_gtf-GRCh37-ensembl             --outTmpDir out/star/build_index/fa-genome-GRCh37_gtf-GRCh37-ensembl/tmp             --genomeFastaFiles out/cat/assembly_ensembl/GRCh37.fa             --sjdbGTFfile out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf

        # Because Star produce a log into the wdir.
		# Edit: 17/09/2020: STAR now write log in output folder. mv no more required
        #mv Log.out out/star/build_index/fa-genome-GRCh37_gtf-GRCh37-ensembl/Log.out
        

[Sat Apr 17 13:59:04 2021]
rule samtools_sam_to_bam_bai_extra:
    input: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.sam
    output: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam.bai
    log: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2371
    reason: Missing output files: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam; Input files updated by another job: out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.sam
    wildcards: tool=samtools/sam_to_bam_bai, extra=_-q_30, filler=bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3


        (
        samtools view -bSh  -q 30 out/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.sam | samtools sort -o out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam
        samtools index out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam
        ) &> out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
        

[Sat Apr 17 13:59:04 2021]
rule ucsc_bedGraphToBigWig:
    input: out/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.BedGraph, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt
    output: out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.bw
    jobid: 37
    reason: Missing output files: out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.bw; Input files updated by another job: out/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.BedGraph, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt
    wildcards: chrominfo_id=chrominfo-hg19, filler=sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph


        bedGraphToBigWig out/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.BedGraph out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.bw
        

[Sat Apr 17 13:59:04 2021]
rule star_pe_extra:
    input: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h_2.fastq.gz, out/star/build_index/fa-genome-GRCh37_gtf-GRCh37-ensembl/Genome, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf
    output: out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h.bam, out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h/Log.final.out
    log: out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h.log
    jobid: 3361
    reason: Missing output files: out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h.bam; Input files updated by another job: out/star/build_index/fa-genome-GRCh37_gtf-GRCh37-ensembl/Genome, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h_2.fastq.gz
    wildcards: tool=star/pe, extin=fastq.gz, extout=bam, extra=_standard, index_id=staridx-hg19-ensembl, gtf_id=gtf-hg19-ensembl, filler=sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h
    threads: 2


        ( WDIR=`pwd`
        mkdir -p out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h
        cd out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h
        STAR             --genomeDir $WDIR/out/star/build_index/fa-genome-GRCh37_gtf-GRCh37-ensembl             --readFilesIn $WDIR/out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h_1.fastq.gz $WDIR/out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h_2.fastq.gz             --sjdbGTFfile $WDIR/out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf             --runThreadN 2             --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate  --outFilterMismatchNoverLmax 0.08 --outFilterMultimapNmax 1 --genomeLoad NoSharedMemory
        mv Aligned.sortedByCoord.out.bam $WDIR/out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h.bam
        rm -rf out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h/_STARgenome ) &> out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h.log
        

[Sat Apr 17 13:59:04 2021]
rule gtftk_coverage_extra_chrominfo_bed_bw:
    input: out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_Jurkat.bed, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.bw, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.bw, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.bw, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.bw
    output: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-sharp_bw-hg19-Orlando2014-Jurkat.txt
    log: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-sharp_bw-hg19-Orlando2014-Jurkat.log
    jobid: 0
    reason: Missing output files: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-sharp_bw-hg19-Orlando2014-Jurkat.txt; Input files updated by another job: out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.bw, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.bw, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.bw, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.bw, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_Jurkat.bed
    wildcards: tool=gtftk/coverage, extra=_-x, chrominfo_id=chrominfo-hg19, bed_list_id=bed-hg19-jurkat-sharp, bw_list_id=bw-hg19-Orlando2014-Jurkat
    threads: 2


        gtftk coverage  -x --inputfile out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_Jurkat.bed --outputfile out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-sharp_bw-hg19-Orlando2014-Jurkat.txt --chrom-info out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt --nb-proc 2 out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.bw out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.bw out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.bw out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.bw &> out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-sharp_bw-hg19-Orlando2014-Jurkat.log
        

[Sat Apr 17 13:59:04 2021]
rule samtools_sam_to_bam_bai_extra:
    input: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.sam
    output: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam.bai
    log: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2378
    reason: Missing output files: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam; Input files updated by another job: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.sam
    wildcards: tool=samtools/sam_to_bam_bai, extra=_-q_30, filler=bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3


        (
        samtools view -bSh  -q 30 out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.sam | samtools sort -o out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam
        samtools index out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam
        ) &> out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
        

[Sat Apr 17 13:59:04 2021]
rule samtools_sam_to_bam_bai_extra:
    input: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.sam
    output: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam.bai
    log: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 2368
    reason: Missing output files: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam; Input files updated by another job: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.sam
    wildcards: tool=samtools/sam_to_bam_bai, extra=_-q_30, filler=bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3


        (
        samtools view -bSh  -q 30 out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.sam | samtools sort -o out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam
        samtools index out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam
        ) &> out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
        

[Sat Apr 17 13:59:04 2021]
rule star_pe_extra:
    input: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM_2.fastq.gz, out/star/build_index/fa-genome-GRCh37_gtf-GRCh37-ensembl/Genome, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf
    output: out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM.bam, out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM/Log.final.out
    log: out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM.log
    jobid: 3363
    reason: Missing output files: out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM.bam; Input files updated by another job: out/star/build_index/fa-genome-GRCh37_gtf-GRCh37-ensembl/Genome, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM_1.fastq.gz, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM_2.fastq.gz
    wildcards: tool=star/pe, extin=fastq.gz, extout=bam, extra=_standard, index_id=staridx-hg19-ensembl, gtf_id=gtf-hg19-ensembl, filler=sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM
    threads: 2


        ( WDIR=`pwd`
        mkdir -p out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM
        cd out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM
        STAR             --genomeDir $WDIR/out/star/build_index/fa-genome-GRCh37_gtf-GRCh37-ensembl             --readFilesIn $WDIR/out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM_1.fastq.gz $WDIR/out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM_2.fastq.gz             --sjdbGTFfile $WDIR/out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf             --runThreadN 2             --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate  --outFilterMismatchNoverLmax 0.08 --outFilterMultimapNmax 1 --genomeLoad NoSharedMemory
        mv Aligned.sortedByCoord.out.bam $WDIR/out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM.bam
        rm -rf out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM/_STARgenome ) &> out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM.log
        

[Sat Apr 17 13:59:04 2021]
rule star_pe_extra:
    input: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h_2.fastq.gz, out/star/build_index/fa-genome-GRCh37_gtf-GRCh37-ensembl/Genome, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf
    output: out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h.bam, out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h/Log.final.out
    log: out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h.log
    jobid: 3364
    reason: Missing output files: out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h.bam; Input files updated by another job: out/star/build_index/fa-genome-GRCh37_gtf-GRCh37-ensembl/Genome, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h_2.fastq.gz
    wildcards: tool=star/pe, extin=fastq.gz, extout=bam, extra=_standard, index_id=staridx-hg19-ensembl, gtf_id=gtf-hg19-ensembl, filler=sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h
    threads: 2


        ( WDIR=`pwd`
        mkdir -p out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h
        cd out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h
        STAR             --genomeDir $WDIR/out/star/build_index/fa-genome-GRCh37_gtf-GRCh37-ensembl             --readFilesIn $WDIR/out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h_1.fastq.gz $WDIR/out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h_2.fastq.gz             --sjdbGTFfile $WDIR/out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf             --runThreadN 2             --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate  --outFilterMismatchNoverLmax 0.08 --outFilterMultimapNmax 1 --genomeLoad NoSharedMemory
        mv Aligned.sortedByCoord.out.bam $WDIR/out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h.bam
        rm -rf out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h/_STARgenome ) &> out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h.log
        

[Sat Apr 17 13:59:04 2021]
rule star_pe_extra:
    input: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM_2.fastq.gz, out/star/build_index/fa-genome-GRCh37_gtf-GRCh37-ensembl/Genome, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf
    output: out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM.bam, out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM/Log.final.out
    log: out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM.log
    jobid: 3362
    reason: Missing output files: out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM.bam; Input files updated by another job: out/star/build_index/fa-genome-GRCh37_gtf-GRCh37-ensembl/Genome, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM_1.fastq.gz, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM_2.fastq.gz
    wildcards: tool=star/pe, extin=fastq.gz, extout=bam, extra=_standard, index_id=staridx-hg19-ensembl, gtf_id=gtf-hg19-ensembl, filler=sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM
    threads: 2


        ( WDIR=`pwd`
        mkdir -p out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM
        cd out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM
        STAR             --genomeDir $WDIR/out/star/build_index/fa-genome-GRCh37_gtf-GRCh37-ensembl             --readFilesIn $WDIR/out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM_1.fastq.gz $WDIR/out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM_2.fastq.gz             --sjdbGTFfile $WDIR/out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf             --runThreadN 2             --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate  --outFilterMismatchNoverLmax 0.08 --outFilterMultimapNmax 1 --genomeLoad NoSharedMemory
        mv Aligned.sortedByCoord.out.bam $WDIR/out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM.bam
        rm -rf out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM/_STARgenome ) &> out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM.log
        

[Sat Apr 17 13:59:04 2021]
rule samtools_sort_extra:
    input: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam
    output: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam
    log: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 3553
    reason: Missing output files: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam; Input files updated by another job: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam
    wildcards: tool=samtools/sort, extra=, filler=samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    threads: 2

samtools sort -@ 2 -T out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam  out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam -o out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam &> out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:04 2021]
rule samtools_sort_extra:
    input: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam
    output: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam
    log: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 3548
    reason: Missing output files: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam; Input files updated by another job: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam
    wildcards: tool=samtools/sort, extra=, filler=samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    threads: 2

samtools sort -@ 2 -T out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam  out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam -o out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam &> out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:04 2021]
rule samtools_sam_to_bam_bai_extra:
    input: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.sam
    output: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam.bai
    log: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 2364
    reason: Missing output files: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam; Input files updated by another job: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.sam
    wildcards: tool=samtools/sam_to_bam_bai, extra=_-q_30, filler=bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3


        (
        samtools view -bSh  -q 30 out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.sam | samtools sort -o out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam
        samtools index out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam
        ) &> out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
        

[Sat Apr 17 13:59:04 2021]
rule samtools_sort_extra:
    input: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam
    output: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam
    log: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 3549
    reason: Missing output files: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam; Input files updated by another job: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam
    wildcards: tool=samtools/sort, extra=, filler=samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    threads: 2

samtools sort -@ 2 -T out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam  out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam -o out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam &> out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:04 2021]
rule samtools_view_sam_to_bam_extra:
    input: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.sam
    output: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.bam
    log: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 3563
    reason: Missing output files: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.bam; Input files updated by another job: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.sam
    wildcards: tool=samtools/view_sam_to_bam, extra=_-q_30, filler=bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3

samtools view -bSh  -q 30 out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.sam -o out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.bam &> out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:04 2021]
rule star_pe_extra:
    input: out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM_1.fastq.gz, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM_2.fastq.gz, out/star/build_index/fa-genome-GRCh37_gtf-GRCh37-ensembl/Genome, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf
    output: out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM.bam, out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM/Log.final.out
    log: out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM.log
    jobid: 3365
    reason: Missing output files: out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM.bam; Input files updated by another job: out/star/build_index/fa-genome-GRCh37_gtf-GRCh37-ensembl/Genome, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM_2.fastq.gz, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf, out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM_1.fastq.gz
    wildcards: tool=star/pe, extin=fastq.gz, extout=bam, extra=_standard, index_id=staridx-hg19-ensembl, gtf_id=gtf-hg19-ensembl, filler=sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM
    threads: 2


        ( WDIR=`pwd`
        mkdir -p out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM
        cd out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM
        STAR             --genomeDir $WDIR/out/star/build_index/fa-genome-GRCh37_gtf-GRCh37-ensembl             --readFilesIn $WDIR/out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM_1.fastq.gz $WDIR/out/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM_2.fastq.gz             --sjdbGTFfile $WDIR/out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf             --runThreadN 2             --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate  --outFilterMismatchNoverLmax 0.08 --outFilterMultimapNmax 1 --genomeLoad NoSharedMemory
        mv Aligned.sortedByCoord.out.bam $WDIR/out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM.bam
        rm -rf out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM/_STARgenome ) &> out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM.log
        

[Sat Apr 17 13:59:04 2021]
rule r_extract_control_sharp_subsets_from_Atak2013:
    input: inp/KalenderAtak2013/Global_Data_RNA-seq_TALL_Isoforms_ATAK.csv.bz2, out/gtftk/get_5p_3p_coords/gtftk/convert_ensembl/gunzip/to-stdout/wget/https/ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.bed, out/sort/_-u_-k1,1_-k2,2n/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_Jurkat.bed, out/sort/_-u_-k1,1_-k2,2n/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_Jurkat.bed
    output: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    jobid: 326
    reason: Missing output files: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed; Input files updated by another job: out/gtftk/get_5p_3p_coords/gtftk/convert_ensembl/gunzip/to-stdout/wget/https/ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.bed, out/sort/_-u_-k1,1_-k2,2n/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_Jurkat.bed, out/sort/_-u_-k1,1_-k2,2n/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_Jurkat.bed

[Sat Apr 17 13:59:04 2021]
rule samtools_view_sam_to_bam_extra:
    input: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.sam
    output: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.bam
    log: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.log
    jobid: 3568
    reason: Missing output files: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.bam; Input files updated by another job: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.sam
    wildcards: tool=samtools/view_sam_to_bam, extra=_-q_30, filler=bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2

samtools view -bSh  -q 30 out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.sam -o out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.bam &> out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:04 2021]
rule samtools_sort_extra:
    input: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam
    output: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam
    log: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 3552
    reason: Missing output files: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam; Input files updated by another job: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam
    wildcards: tool=samtools/sort, extra=, filler=samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    threads: 2

samtools sort -@ 2 -T out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam  out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam -o out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam &> out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:04 2021]
rule samtools_sort_extra:
    input: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam
    output: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam
    log: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 3554
    reason: Missing output files: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam; Input files updated by another job: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam
    wildcards: tool=samtools/sort, extra=, filler=samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    threads: 2

samtools sort -@ 2 -T out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam  out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam -o out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam &> out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:04 2021]
rule samtools_view_sam_to_bam_extra:
    input: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.sam
    output: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.bam
    log: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 3560
    reason: Missing output files: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.bam; Input files updated by another job: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.sam
    wildcards: tool=samtools/view_sam_to_bam, extra=_-q_30, filler=bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3

samtools view -bSh  -q 30 out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.sam -o out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.bam &> out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:04 2021]
rule samtools_view_sam_to_bam_extra:
    input: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.sam
    output: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.bam
    log: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.log
    jobid: 3565
    reason: Missing output files: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.bam; Input files updated by another job: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.sam
    wildcards: tool=samtools/view_sam_to_bam, extra=_-q_30, filler=bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3

samtools view -bSh  -q 30 out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.sam -o out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.bam &> out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:04 2021]
rule samtools_view_sam_to_bam_extra:
    input: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.sam
    output: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.bam
    log: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.log
    jobid: 3564
    reason: Missing output files: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.bam; Input files updated by another job: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.sam
    wildcards: tool=samtools/view_sam_to_bam, extra=_-q_30, filler=bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7

samtools view -bSh  -q 30 out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.sam -o out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.bam &> out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:04 2021]
rule samtools_sort_extra:
    input: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam
    output: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam
    log: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 3550
    reason: Missing output files: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam; Input files updated by another job: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam
    wildcards: tool=samtools/sort, extra=, filler=samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    threads: 2

samtools sort -@ 2 -T out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam  out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam -o out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam &> out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:04 2021]
rule samtools_sort_extra:
    input: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam
    output: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam
    log: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 3556
    reason: Missing output files: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam; Input files updated by another job: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam
    wildcards: tool=samtools/sort, extra=, filler=samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    threads: 2

samtools sort -@ 2 -T out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam  out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam -o out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam &> out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:04 2021]
rule samtools_sam_to_bam_bai_extra:
    input: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.sam
    output: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam.bai
    log: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2380
    reason: Missing output files: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam; Input files updated by another job: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.sam
    wildcards: tool=samtools/sam_to_bam_bai, extra=_-q_30, filler=bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3


        (
        samtools view -bSh  -q 30 out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.sam | samtools sort -o out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam
        samtools index out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam
        ) &> out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
        

[Sat Apr 17 13:59:04 2021]
rule samtools_view_sam_to_bam_extra:
    input: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.sam
    output: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.bam
    log: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 3561
    reason: Missing output files: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.bam; Input files updated by another job: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.sam
    wildcards: tool=samtools/view_sam_to_bam, extra=_-q_30, filler=bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3

samtools view -bSh  -q 30 out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.sam -o out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.bam &> out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:04 2021]
rule samtools_sort_extra:
    input: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam
    output: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam
    log: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 3551
    reason: Missing output files: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam; Input files updated by another job: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam
    wildcards: tool=samtools/sort, extra=, filler=samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    threads: 2

samtools sort -@ 2 -T out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam  out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam -o out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam &> out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:04 2021]
rule gtftk_coverage_extra_chrominfo_bed_bw:
    input: out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_Jurkat.bed, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.bw, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.bw, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.bw, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.bw
    output: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-broad_bw-hg19-Orlando2014-Jurkat.txt
    log: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-broad_bw-hg19-Orlando2014-Jurkat.log
    jobid: 4
    reason: Missing output files: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-broad_bw-hg19-Orlando2014-Jurkat.txt; Input files updated by another job: out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.bw, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.bw, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.bw, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.bw, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_Jurkat.bed
    wildcards: tool=gtftk/coverage, extra=_-x, chrominfo_id=chrominfo-hg19, bed_list_id=bed-hg19-jurkat-broad, bw_list_id=bw-hg19-Orlando2014-Jurkat
    threads: 2


        gtftk coverage  -x --inputfile out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_Jurkat.bed --outputfile out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-broad_bw-hg19-Orlando2014-Jurkat.txt --chrom-info out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt --nb-proc 2 out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.bw out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.bw out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.bw out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.bw &> out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-broad_bw-hg19-Orlando2014-Jurkat.log
        

[Sat Apr 17 13:59:04 2021]
rule samtools_sam_to_bam_bai_extra:
    input: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.sam
    output: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam.bai
    log: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 2366
    reason: Missing output files: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam; Input files updated by another job: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.sam
    wildcards: tool=samtools/sam_to_bam_bai, extra=_-q_30, filler=bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3


        (
        samtools view -bSh  -q 30 out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.sam | samtools sort -o out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam
        samtools index out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam
        ) &> out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
        

[Sat Apr 17 13:59:04 2021]
rule samtools_view_sam_to_bam_extra:
    input: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.sam
    output: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.bam
    log: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.log
    jobid: 3447
    reason: Missing output files: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.bam; Input files updated by another job: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.sam
    wildcards: tool=samtools/view_sam_to_bam, extra=_-q_30, filler=bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3

samtools view -bSh  -q 30 out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.sam -o out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.bam &> out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.log

[Sat Apr 17 13:59:04 2021]
rule samtools_sam_to_bam_bai_extra:
    input: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.sam
    output: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam.bai
    log: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 2370
    reason: Missing output files: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam; Input files updated by another job: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.sam
    wildcards: tool=samtools/sam_to_bam_bai, extra=_-q_30, filler=bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3


        (
        samtools view -bSh  -q 30 out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.sam | samtools sort -o out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam
        samtools index out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam
        ) &> out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
        

[Sat Apr 17 13:59:04 2021]
rule sickle_se_extra:
    input: out/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.fastq.gz
    output: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.fastq.gz
    log: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.fastq.gz.log
    jobid: 3673
    reason: Missing output files: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.fastq.gz; Input files updated by another job: out/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.fastq.gz
    wildcards: tool=sickle/se, extra=_-t_sanger_-q_20, filler=ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2, ext=fastq.gz

sickle se -f out/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.fastq.gz  -t sanger -q 20 -g -o out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.fastq.gz &> out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.fastq.gz.log

[Sat Apr 17 13:59:04 2021]
rule samtools_view_sam_to_bam_extra:
    input: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.sam
    output: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.bam
    log: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.log
    jobid: 3394
    reason: Missing output files: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.bam; Input files updated by another job: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.sam
    wildcards: tool=samtools/view_sam_to_bam, extra=_-q_30, filler=bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2

samtools view -bSh  -q 30 out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.sam -o out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.bam &> out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:04 2021]
rule samtools_sam_to_bam_bai_extra:
    input: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.sam
    output: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam.bai
    log: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2372
    reason: Missing output files: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam; Input files updated by another job: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.sam
    wildcards: tool=samtools/sam_to_bam_bai, extra=_-q_30, filler=bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3


        (
        samtools view -bSh  -q 30 out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.sam | samtools sort -o out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam
        samtools index out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam
        ) &> out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
        

[Sat Apr 17 13:59:04 2021]
rule samtools_view_sam_to_bam_extra:
    input: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.sam
    output: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.bam
    log: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.log
    jobid: 3442
    reason: Missing output files: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.bam; Input files updated by another job: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.sam
    wildcards: tool=samtools/view_sam_to_bam, extra=_-q_30, filler=bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3

samtools view -bSh  -q 30 out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.sam -o out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.bam &> out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.log

[Sat Apr 17 13:59:04 2021]
rule sickle_se_extra:
    input: out/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.fastq.gz
    output: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.fastq.gz
    log: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.fastq.gz.log
    jobid: 3672
    reason: Missing output files: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.fastq.gz; Input files updated by another job: out/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.fastq.gz
    wildcards: tool=sickle/se, extra=_-t_sanger_-q_20, filler=ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3, ext=fastq.gz

sickle se -f out/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.fastq.gz  -t sanger -q 20 -g -o out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.fastq.gz &> out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.fastq.gz.log

[Sat Apr 17 13:59:04 2021]
rule samtools_view_sam_to_bam_extra:
    input: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.sam
    output: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.bam
    log: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 3562
    reason: Missing output files: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.bam; Input files updated by another job: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.sam
    wildcards: tool=samtools/view_sam_to_bam, extra=_-q_30, filler=bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3

samtools view -bSh  -q 30 out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.sam -o out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.bam &> out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:04 2021]
rule samtools_view_sam_to_bam_extra:
    input: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.sam
    output: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.bam
    log: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.log
    jobid: 3567
    reason: Missing output files: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.bam; Input files updated by another job: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.sam
    wildcards: tool=samtools/view_sam_to_bam, extra=_-q_30, filler=bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI

samtools view -bSh  -q 30 out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.sam -o out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.bam &> out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:04 2021]
rule samtools_view_sam_to_bam_extra:
    input: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.sam
    output: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.bam
    log: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.log
    jobid: 3446
    reason: Missing output files: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.bam; Input files updated by another job: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.sam
    wildcards: tool=samtools/view_sam_to_bam, extra=_-q_30, filler=bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3

samtools view -bSh  -q 30 out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.sam -o out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.bam &> out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.log

[Sat Apr 17 13:59:04 2021]
rule samtools_sort_extra:
    input: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam
    output: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam
    log: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 3555
    reason: Missing output files: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam; Input files updated by another job: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam
    wildcards: tool=samtools/sort, extra=, filler=samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    threads: 2

samtools sort -@ 2 -T out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam  out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam -o out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam &> out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:04 2021]
rule sickle_se_extra:
    input: out/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.fastq.gz
    output: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.fastq.gz
    log: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.fastq.gz.log
    jobid: 3683
    reason: Missing output files: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.fastq.gz; Input files updated by another job: out/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.fastq.gz
    wildcards: tool=sickle/se, extra=_-t_sanger_-q_20, filler=ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3, ext=fastq.gz

sickle se -f out/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.fastq.gz  -t sanger -q 20 -g -o out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.fastq.gz &> out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.fastq.gz.log

[Sat Apr 17 13:59:04 2021]
rule samtools_view_sam_to_bam_extra:
    input: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.sam
    output: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.bam
    log: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.log
    jobid: 3566
    reason: Missing output files: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.bam; Input files updated by another job: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.sam
    wildcards: tool=samtools/view_sam_to_bam, extra=_-q_30, filler=bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2

samtools view -bSh  -q 30 out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.sam -o out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.bam &> out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:04 2021]
rule samtools_sam_to_bam_bai_extra:
    input: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.sam
    output: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam.bai
    log: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2376
    reason: Missing output files: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam; Input files updated by another job: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.sam
    wildcards: tool=samtools/sam_to_bam_bai, extra=_-q_30, filler=bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3


        (
        samtools view -bSh  -q 30 out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.sam | samtools sort -o out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam
        samtools index out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam
        ) &> out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
        

[Sat Apr 17 13:59:04 2021]
rule samtools_sort_extra:
    input: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam
    output: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam
    log: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 3557
    reason: Missing output files: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam; Input files updated by another job: out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam
    wildcards: tool=samtools/sort, extra=, filler=samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    threads: 2

samtools sort -@ 2 -T out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam  out/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam -o out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam &> out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:04 2021]
rule star_se_extra:
    input: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM.fastq.gz, out/star/build_index/fa-genome-GRCh37_gtf-GRCh37-ensembl/Genome, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf
    output: out/star/se_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM.bam, out/star/se_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM/Log.final.out
    jobid: 3366
    reason: Missing output files: out/star/se_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM.bam; Input files updated by another job: out/star/build_index/fa-genome-GRCh37_gtf-GRCh37-ensembl/Genome, out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf, out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM.fastq.gz
    wildcards: tool=star/se, extin=fastq.gz, extout=bam, extra=_standard, index_id=staridx-hg19-ensembl, gtf_id=gtf-hg19-ensembl, filler=sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM
    threads: 2


        WDIR=`pwd`
        mkdir -p out/star/se_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM
        cd out/star/se_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM
        STAR             --genomeDir $WDIR/out/star/build_index/fa-genome-GRCh37_gtf-GRCh37-ensembl             -c --readFilesIn $WDIR/out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM.fastq.gz            --sjdbGTFfile $WDIR/out/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/release-67/gtf/homo_sapiens/Homo_sapiens.GRCh37.67.gtf             --runThreadN 2             --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate  --outFilterMismatchNoverLmax 0.08 --outFilterMultimapNmax 1 --genomeLoad NoSharedMemory
        mv Aligned.sortedByCoord.out.bam $WDIR/out/star/se_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM.bam
        rm -rf out/star/se_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM/_STARgenome
        

[Sat Apr 17 13:59:04 2021]
rule samtools_sam_to_bam_bai_extra:
    input: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.sam
    output: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam.bai
    log: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2382
    reason: Missing output files: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam; Input files updated by another job: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.sam
    wildcards: tool=samtools/sam_to_bam_bai, extra=_-q_30, filler=bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3


        (
        samtools view -bSh  -q 30 out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.sam | samtools sort -o out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam
        samtools index out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam
        ) &> out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
        

[Sat Apr 17 13:59:04 2021]
rule samtools_view_sam_to_bam_extra:
    input: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.sam
    output: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.bam
    log: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.log
    jobid: 3445
    reason: Missing output files: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.bam; Input files updated by another job: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.sam
    wildcards: tool=samtools/view_sam_to_bam, extra=_-q_30, filler=bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3

samtools view -bSh  -q 30 out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.sam -o out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.bam &> out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.log

[Sat Apr 17 13:59:04 2021]
rule samtools_sam_to_bam_bai_extra:
    input: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.sam
    output: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam.bai
    log: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2374
    reason: Missing output files: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam; Input files updated by another job: out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.sam
    wildcards: tool=samtools/sam_to_bam_bai, extra=_-q_30, filler=bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3


        (
        samtools view -bSh  -q 30 out/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.sam | samtools sort -o out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam
        samtools index out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam
        ) &> out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
        

[Sat Apr 17 13:59:04 2021]
rule samtools_sort_extra:
    input: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.bam
    output: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.bam
    log: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.log
    jobid: 3397
    reason: Missing output files: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.bam; Input files updated by another job: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.bam
    wildcards: tool=samtools/sort, extra=, filler=samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3
    threads: 2

samtools sort -@ 2 -T out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.bam  out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.bam -o out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.bam &> out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.log

[Sat Apr 17 13:59:04 2021]
rule samtools_sort_extra:
    input: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.bam
    output: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.bam
    log: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.log
    jobid: 3500
    reason: Missing output files: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.bam; Input files updated by another job: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.bam
    wildcards: tool=samtools/sort, extra=, filler=samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3
    threads: 2

samtools sort -@ 2 -T out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.bam  out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.bam -o out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.bam &> out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:04 2021]
rule samtools_index:
    input: out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM.bam
    output: out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM.bam, out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM.bam.bai
    log: out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM.log
    jobid: 2385
    benchmark: out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM.benchmark.tsv
    reason: Missing output files: out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM.bam; Input files updated by another job: out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM.bam
    wildcards: filler=star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM


        (ln -srf out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM.bam out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM.bam
        samtools index out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM.bam) &> out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM.log
        

[Sat Apr 17 13:59:04 2021]
rule deepTools_spikeIn_bamCoverage:
    input: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam
    output: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw
    jobid: 341
    reason: Missing output files: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw; Input files updated by another job: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam
    wildcards: tool=deepTools/spikeIn_bamCoverage, assembly_exo=BDGP6, extra=, filler1=samtools/sam_to_bam_bai_-q_30/bowtie2/pe_, assembly_endo=hg19, filler2=/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    threads: 2


        nb_reads_in_exo=`samtools view -c out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam`
        sf=`bc -l <<<"100000/$nb_reads_in_exo"`
        bamCoverage -b out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam --numberOfProcessors 2  --normalizeUsing None --scaleFactor $sf -o out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw
        

[Sat Apr 17 13:59:04 2021]
rule samtools_sort_extra:
    input: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.bam
    output: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.bam
    log: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.log
    jobid: 3503
    reason: Missing output files: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.bam; Input files updated by another job: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.bam
    wildcards: tool=samtools/sort, extra=, filler=samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2
    threads: 2

samtools sort -@ 2 -T out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.bam  out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.bam -o out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.bam &> out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:04 2021]
rule samtools_index:
    input: out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h.bam
    output: out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h.bam, out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h.bam.bai
    log: out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h.log
    jobid: 2387
    benchmark: out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h.benchmark.tsv
    reason: Missing output files: out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h.bam; Input files updated by another job: out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h.bam
    wildcards: filler=star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h


        (ln -srf out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h.bam out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h.bam
        samtools index out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h.bam) &> out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h.log
        

[Sat Apr 17 13:59:04 2021]
rule bowtie2_single_end_extra:
    input: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2
    output: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.sam, out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3_single.fastq.gz
    log: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.log
    jobid: 3655
    reason: Missing output files: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.sam; Input files updated by another job: out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2
    wildcards: tool=bowtie2/se, extra=, index=hg19, filler=sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3
    threads: 2


        bowtie2 -p 2 -x out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome             -U out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.fastq.gz             --un-gz out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3_single.fastq.gz             -S out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.sam                         2> out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.log
        

[Sat Apr 17 13:59:04 2021]
rule samtools_sort_extra:
    input: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.bam
    output: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.bam
    log: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 3497
    reason: Missing output files: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.bam; Input files updated by another job: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.bam
    wildcards: tool=samtools/sort, extra=, filler=samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3
    threads: 2

samtools sort -@ 2 -T out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.bam  out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.bam -o out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.bam &> out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:04 2021]
rule samtools_index:
    input: out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM.bam
    output: out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM.bam, out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM.bam.bai
    log: out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM.log
    jobid: 2386
    benchmark: out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM.benchmark.tsv
    reason: Missing output files: out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM.bam; Input files updated by another job: out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM.bam
    wildcards: filler=star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM


        (ln -srf out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM.bam out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM.bam
        samtools index out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM.bam) &> out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM.log
        

[Sat Apr 17 13:59:04 2021]
rule deepTools_spikeIn_bamCoverage:
    input: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam
    output: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    jobid: 335
    reason: Missing output files: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw; Input files updated by another job: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam
    wildcards: tool=deepTools/spikeIn_bamCoverage, assembly_exo=BDGP6, extra=, filler1=samtools/sam_to_bam_bai_-q_30/bowtie2/pe_, assembly_endo=hg19, filler2=/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    threads: 2


        nb_reads_in_exo=`samtools view -c out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam`
        sf=`bc -l <<<"100000/$nb_reads_in_exo"`
        bamCoverage -b out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam --numberOfProcessors 2  --normalizeUsing None --scaleFactor $sf -o out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
        

[Sat Apr 17 13:59:04 2021]
rule deepTools_spikeIn_bamCoverage:
    input: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam
    output: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw
    jobid: 342
    reason: Missing output files: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw; Input files updated by another job: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam
    wildcards: tool=deepTools/spikeIn_bamCoverage, assembly_exo=BDGP6, extra=, filler1=samtools/sam_to_bam_bai_-q_30/bowtie2/pe_, assembly_endo=hg19, filler2=/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    threads: 2


        nb_reads_in_exo=`samtools view -c out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam`
        sf=`bc -l <<<"100000/$nb_reads_in_exo"`
        bamCoverage -b out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam --numberOfProcessors 2  --normalizeUsing None --scaleFactor $sf -o out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw
        

[Sat Apr 17 13:59:04 2021]
rule samtools_sort_extra:
    input: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.bam
    output: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.bam
    log: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.log
    jobid: 3393
    reason: Missing output files: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.bam; Input files updated by another job: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.bam
    wildcards: tool=samtools/sort, extra=, filler=samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3
    threads: 2

samtools sort -@ 2 -T out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.bam  out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.bam -o out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.bam &> out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.log

[Sat Apr 17 13:59:04 2021]
rule deepTools_spikeIn_bamCoverage:
    input: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam
    output: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw
    jobid: 334
    reason: Missing output files: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw; Input files updated by another job: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam
    wildcards: tool=deepTools/spikeIn_bamCoverage, assembly_exo=BDGP6, extra=, filler1=samtools/sam_to_bam_bai_-q_30/bowtie2/pe_, assembly_endo=hg19, filler2=/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    threads: 2


        nb_reads_in_exo=`samtools view -c out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam`
        sf=`bc -l <<<"100000/$nb_reads_in_exo"`
        bamCoverage -b out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam --numberOfProcessors 2  --normalizeUsing None --scaleFactor $sf -o out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw
        

[Sat Apr 17 13:59:05 2021]
rule samtools_index:
    input: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam
    output: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam.bai
    log: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 3487
    benchmark: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam.bai, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam; Input files updated by another job: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam
    wildcards: filler=samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3


        (ln -srf out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam
        samtools index out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam) &> out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
        

[Sat Apr 17 13:59:05 2021]
rule samtools_index:
    input: out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h.bam
    output: out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h.bam, out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h.bam.bai
    log: out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h.log
    jobid: 2384
    benchmark: out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h.benchmark.tsv
    reason: Missing output files: out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h.bam; Input files updated by another job: out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h.bam
    wildcards: filler=star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h


        (ln -srf out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h.bam out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h.bam
        samtools index out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h.bam) &> out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h.log
        

[Sat Apr 17 13:59:05 2021]
rule deepTools_spikeIn_bamCoverage:
    input: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam
    output: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw
    jobid: 343
    reason: Missing output files: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw; Input files updated by another job: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam
    wildcards: tool=deepTools/spikeIn_bamCoverage, assembly_exo=BDGP6, extra=, filler1=samtools/sam_to_bam_bai_-q_30/bowtie2/pe_, assembly_endo=hg19, filler2=/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    threads: 2


        nb_reads_in_exo=`samtools view -c out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam`
        sf=`bc -l <<<"100000/$nb_reads_in_exo"`
        bamCoverage -b out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam --numberOfProcessors 2  --normalizeUsing None --scaleFactor $sf -o out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw
        

[Sat Apr 17 13:59:05 2021]
rule samtools_index:
    input: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam
    output: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam.bai
    log: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 3490
    benchmark: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam.bai, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam; Input files updated by another job: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam
    wildcards: filler=samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3


        (ln -srf out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam
        samtools index out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam) &> out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
        

[Sat Apr 17 13:59:05 2021]
rule samtools_index:
    input: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam
    output: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam.bai
    log: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 3492
    benchmark: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam.bai, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam; Input files updated by another job: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam
    wildcards: filler=samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3


        (ln -srf out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam
        samtools index out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam) &> out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
        

[Sat Apr 17 13:59:05 2021]
rule samtools_sort_extra:
    input: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.bam
    output: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.bam
    log: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 3495
    reason: Missing output files: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.bam; Input files updated by another job: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.bam
    wildcards: tool=samtools/sort, extra=, filler=samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3
    threads: 2

samtools sort -@ 2 -T out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.bam  out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.bam -o out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.bam &> out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_spikeIn_bamCoverage:
    input: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam
    output: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw
    jobid: 336
    reason: Missing output files: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw; Input files updated by another job: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam
    wildcards: tool=deepTools/spikeIn_bamCoverage, assembly_exo=BDGP6, extra=, filler1=samtools/sam_to_bam_bai_-q_30/bowtie2/pe_, assembly_endo=hg19, filler2=/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    threads: 2


        nb_reads_in_exo=`samtools view -c out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam`
        sf=`bc -l <<<"100000/$nb_reads_in_exo"`
        bamCoverage -b out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam --numberOfProcessors 2  --normalizeUsing None --scaleFactor $sf -o out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw
        

[Sat Apr 17 13:59:05 2021]
rule samtools_index:
    input: out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM.bam
    output: out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM.bam, out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM.bam.bai
    log: out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM.log
    jobid: 2388
    benchmark: out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM.benchmark.tsv
    reason: Missing output files: out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM.bam; Input files updated by another job: out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM.bam
    wildcards: filler=star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM


        (ln -srf out/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM.bam out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM.bam
        samtools index out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM.bam) &> out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM.log
        

[Sat Apr 17 13:59:05 2021]
rule samtools_index:
    input: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam
    output: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam.bai
    log: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 3486
    benchmark: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam.bai; Input files updated by another job: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam
    wildcards: filler=samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3


        (ln -srf out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam
        samtools index out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam) &> out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
        

[Sat Apr 17 13:59:05 2021]
rule deepTools_spikeIn_bamCoverage:
    input: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam
    output: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw
    jobid: 340
    reason: Missing output files: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw; Input files updated by another job: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam
    wildcards: tool=deepTools/spikeIn_bamCoverage, assembly_exo=BDGP6, extra=, filler1=samtools/sam_to_bam_bai_-q_30/bowtie2/pe_, assembly_endo=hg19, filler2=/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    threads: 2


        nb_reads_in_exo=`samtools view -c out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam`
        sf=`bc -l <<<"100000/$nb_reads_in_exo"`
        bamCoverage -b out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam --numberOfProcessors 2  --normalizeUsing None --scaleFactor $sf -o out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw
        

[Sat Apr 17 13:59:05 2021]
rule samtools_index:
    input: out/star/se_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM.bam
    output: out/samtools/index/star/se_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM.bam, out/samtools/index/star/se_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM.bam.bai
    log: out/samtools/index/star/se_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM.log
    jobid: 2389
    benchmark: out/samtools/index/star/se_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM.benchmark.tsv
    reason: Missing output files: out/samtools/index/star/se_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM.bam; Input files updated by another job: out/star/se_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM.bam
    wildcards: filler=star/se_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM


        (ln -srf out/star/se_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM.bam out/samtools/index/star/se_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM.bam
        samtools index out/samtools/index/star/se_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM.bam) &> out/samtools/index/star/se_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM.log
        

[Sat Apr 17 13:59:05 2021]
rule deepTools_spikeIn_bamCoverage:
    input: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam
    output: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw
    jobid: 338
    reason: Missing output files: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw; Input files updated by another job: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam
    wildcards: tool=deepTools/spikeIn_bamCoverage, assembly_exo=BDGP6, extra=, filler1=samtools/sam_to_bam_bai_-q_30/bowtie2/pe_, assembly_endo=hg19, filler2=/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    threads: 2


        nb_reads_in_exo=`samtools view -c out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam`
        sf=`bc -l <<<"100000/$nb_reads_in_exo"`
        bamCoverage -b out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam --numberOfProcessors 2  --normalizeUsing None --scaleFactor $sf -o out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw
        

[Sat Apr 17 13:59:05 2021]
rule samtools_sort_extra:
    input: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.bam
    output: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.bam
    log: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.log
    jobid: 3335
    reason: Missing output files: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.bam; Input files updated by another job: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.bam
    wildcards: tool=samtools/sort, extra=, filler=samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2
    threads: 2

samtools sort -@ 2 -T out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.bam  out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.bam -o out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.bam &> out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:05 2021]
rule samtools_sort_extra:
    input: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.bam
    output: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.bam
    log: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.log
    jobid: 3501
    reason: Missing output files: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.bam; Input files updated by another job: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.bam
    wildcards: tool=samtools/sort, extra=, filler=samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2
    threads: 2

samtools sort -@ 2 -T out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.bam  out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.bam -o out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.bam &> out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:05 2021]
rule samtools_index:
    input: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam
    output: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam.bai
    log: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 3491
    benchmark: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam.bai, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam; Input files updated by another job: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam
    wildcards: filler=samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3


        (ln -srf out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam
        samtools index out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam) &> out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
        

[Sat Apr 17 13:59:05 2021]
rule samtools_index:
    input: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam
    output: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam.bai
    log: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 3484
    benchmark: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam.bai, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam; Input files updated by another job: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam
    wildcards: filler=samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3


        (ln -srf out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam
        samtools index out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam) &> out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
        

[Sat Apr 17 13:59:05 2021]
rule samtools_index:
    input: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam
    output: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam.bai
    log: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 3485
    benchmark: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam.bai; Input files updated by another job: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam
    wildcards: filler=samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3


        (ln -srf out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam
        samtools index out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam) &> out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
        

[Sat Apr 17 13:59:05 2021]
rule samtools_index:
    input: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam
    output: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam.bai
    log: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 3483
    benchmark: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam.bai; Input files updated by another job: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam
    wildcards: filler=samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3


        (ln -srf out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam
        samtools index out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam) &> out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
        

[Sat Apr 17 13:59:05 2021]
rule samtools_index:
    input: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam
    output: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam.bai
    log: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 3488
    benchmark: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam.bai; Input files updated by another job: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam
    wildcards: filler=samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3


        (ln -srf out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam
        samtools index out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam) &> out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
        

[Sat Apr 17 13:59:05 2021]
rule deepTools_spikeIn_bamCoverage:
    input: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam
    output: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw
    jobid: 337
    reason: Missing output files: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw; Input files updated by another job: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam
    wildcards: tool=deepTools/spikeIn_bamCoverage, assembly_exo=BDGP6, extra=, filler1=samtools/sam_to_bam_bai_-q_30/bowtie2/pe_, assembly_endo=hg19, filler2=/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    threads: 2


        nb_reads_in_exo=`samtools view -c out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam`
        sf=`bc -l <<<"100000/$nb_reads_in_exo"`
        bamCoverage -b out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam --numberOfProcessors 2  --normalizeUsing None --scaleFactor $sf -o out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw
        

[Sat Apr 17 13:59:05 2021]
rule samtools_sort_extra:
    input: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.bam
    output: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.bam
    log: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.log
    jobid: 3502
    reason: Missing output files: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.bam; Input files updated by another job: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.bam
    wildcards: tool=samtools/sort, extra=, filler=samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI
    threads: 2

samtools sort -@ 2 -T out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.bam  out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.bam -o out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.bam &> out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_spikeIn_bamCoverage:
    input: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam
    output: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw
    jobid: 339
    reason: Missing output files: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw; Input files updated by another job: out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam, out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam
    wildcards: tool=deepTools/spikeIn_bamCoverage, assembly_exo=BDGP6, extra=, filler1=samtools/sam_to_bam_bai_-q_30/bowtie2/pe_, assembly_endo=hg19, filler2=/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    threads: 2


        nb_reads_in_exo=`samtools view -c out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_BDGP6/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam`
        sf=`bc -l <<<"100000/$nb_reads_in_exo"`
        bamCoverage -b out/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam --numberOfProcessors 2  --normalizeUsing None --scaleFactor $sf -o out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw
        

[Sat Apr 17 13:59:05 2021]
rule samtools_sort_extra:
    input: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.bam
    output: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.bam
    log: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 3496
    reason: Missing output files: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.bam; Input files updated by another job: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.bam
    wildcards: tool=samtools/sort, extra=, filler=samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3
    threads: 2

samtools sort -@ 2 -T out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.bam  out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.bam -o out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.bam &> out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule samtools_sort_extra:
    input: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.bam
    output: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.bam
    log: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.log
    jobid: 3499
    reason: Missing output files: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.bam; Input files updated by another job: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.bam
    wildcards: tool=samtools/sort, extra=, filler=samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7
    threads: 2

samtools sort -@ 2 -T out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.bam  out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.bam -o out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.bam &> out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:05 2021]
rule samtools_sort_extra:
    input: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.bam
    output: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.bam
    log: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 3498
    reason: Missing output files: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.bam; Input files updated by another job: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.bam
    wildcards: tool=samtools/sort, extra=, filler=samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3
    threads: 2

samtools sort -@ 2 -T out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.bam  out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.bam -o out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.bam &> out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule samtools_sort_extra:
    input: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.bam
    output: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.bam
    log: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.log
    jobid: 3396
    reason: Missing output files: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.bam; Input files updated by another job: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.bam
    wildcards: tool=samtools/sort, extra=, filler=samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3
    threads: 2

samtools sort -@ 2 -T out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.bam  out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.bam -o out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.bam &> out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule bowtie2_single_end_extra:
    input: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2
    output: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.sam, out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2_single.fastq.gz
    log: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.log
    jobid: 3656
    reason: Missing output files: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.sam; Input files updated by another job: out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2
    wildcards: tool=bowtie2/se, extra=, index=hg19, filler=sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2
    threads: 2


        bowtie2 -p 2 -x out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome             -U out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.fastq.gz             --un-gz out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2_single.fastq.gz             -S out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.sam                         2> out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.log
        

[Sat Apr 17 13:59:05 2021]
rule bowtie2_single_end_extra:
    input: out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.fastq.gz, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2
    output: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.sam, out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3_single.fastq.gz
    log: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.log
    jobid: 3666
    reason: Missing output files: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.sam; Input files updated by another job: out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.2.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.3.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.4.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.rev.1.bt2, out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.2.bt2, out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.fastq.gz
    wildcards: tool=bowtie2/se, extra=, index=hg19, filler=sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3
    threads: 2


        bowtie2 -p 2 -x out/tar/xvzf_igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome             -U out/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.fastq.gz             --un-gz out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3_single.fastq.gz             -S out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.sam                         2> out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.log
        

[Sat Apr 17 13:59:05 2021]
rule samtools_index:
    input: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam
    output: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam.bai
    log: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 3489
    benchmark: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam.bai, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam; Input files updated by another job: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam
    wildcards: filler=samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3


        (ln -srf out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam
        samtools index out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam) &> out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
        

[Sat Apr 17 13:59:05 2021]
rule samtools_sort_extra:
    input: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.bam
    output: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.bam
    log: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.log
    jobid: 3398
    reason: Missing output files: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.bam; Input files updated by another job: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.bam
    wildcards: tool=samtools/sort, extra=, filler=samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3
    threads: 2

samtools sort -@ 2 -T out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.bam  out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.bam -o out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.bam &> out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
localrule ln_alias:
    input: out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM.bam
    output: out/ln/alias/sst/all_samples/hg19/bam/Loucy_PBIT_5h_10uM.bam
    jobid: 351
    reason: Missing output files: out/ln/alias/sst/all_samples/hg19/bam/Loucy_PBIT_5h_10uM.bam; Input files updated by another job: out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM.bam
    wildcards: id=sst/all_samples/hg19/bam/Loucy_PBIT_5h_10uM.bam
    priority: 10

ln -srf 'out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5h_10uM.bam' out/ln/alias/sst/all_samples/hg19/bam/Loucy_PBIT_5h_10uM.bam

[Sat Apr 17 13:59:05 2021]
localrule ln_alias:
    input: out/samtools/index/star/se_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM.bam
    output: out/ln/alias/sst/all_samples/hg19/bam/Loucy_PBIT_24h_10uM.bam
    jobid: 352
    reason: Missing output files: out/ln/alias/sst/all_samples/hg19/bam/Loucy_PBIT_24h_10uM.bam; Input files updated by another job: out/samtools/index/star/se_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM.bam
    wildcards: id=sst/all_samples/hg19/bam/Loucy_PBIT_24h_10uM.bam
    priority: 10

ln -srf 'out/samtools/index/star/se_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24h_10uM.bam' out/ln/alias/sst/all_samples/hg19/bam/Loucy_PBIT_24h_10uM.bam

[Sat Apr 17 13:59:05 2021]
localrule ln_alias:
    input: out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h.bam
    output: out/ln/alias/sst/all_samples/hg19/bam/Jurkat_DMSO_5h.bam
    jobid: 347
    reason: Missing output files: out/ln/alias/sst/all_samples/hg19/bam/Jurkat_DMSO_5h.bam; Input files updated by another job: out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h.bam
    wildcards: id=sst/all_samples/hg19/bam/Jurkat_DMSO_5h.bam
    priority: 10

ln -srf 'out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_5h.bam' out/ln/alias/sst/all_samples/hg19/bam/Jurkat_DMSO_5h.bam

[Sat Apr 17 13:59:05 2021]
localrule ln_alias:
    input: out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h.bam
    output: out/ln/alias/sst/all_samples/hg19/bam/Loucy_DMSO_5h.bam
    jobid: 350
    reason: Missing output files: out/ln/alias/sst/all_samples/hg19/bam/Loucy_DMSO_5h.bam; Input files updated by another job: out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h.bam
    wildcards: id=sst/all_samples/hg19/bam/Loucy_DMSO_5h.bam
    priority: 10

ln -srf 'out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_5h.bam' out/ln/alias/sst/all_samples/hg19/bam/Loucy_DMSO_5h.bam

[Sat Apr 17 13:59:05 2021]
localrule ln_alias:
    input: out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM.bam
    output: out/ln/alias/sst/all_samples/hg19/bam/Jurkat_PBIT_5h_10uM.bam
    jobid: 348
    reason: Missing output files: out/ln/alias/sst/all_samples/hg19/bam/Jurkat_PBIT_5h_10uM.bam; Input files updated by another job: out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM.bam
    wildcards: id=sst/all_samples/hg19/bam/Jurkat_PBIT_5h_10uM.bam
    priority: 10

ln -srf 'out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5h_10uM.bam' out/ln/alias/sst/all_samples/hg19/bam/Jurkat_PBIT_5h_10uM.bam

[Sat Apr 17 13:59:05 2021]
localrule ln_alias:
    input: out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM.bam
    output: out/ln/alias/sst/all_samples/hg19/bam/Jurkat_PBIT_24h_10uM.bam
    jobid: 349
    reason: Missing output files: out/ln/alias/sst/all_samples/hg19/bam/Jurkat_PBIT_24h_10uM.bam; Input files updated by another job: out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM.bam
    wildcards: id=sst/all_samples/hg19/bam/Jurkat_PBIT_24h_10uM.bam
    priority: 10

ln -srf 'out/samtools/index/star/pe_fastq.gz_to_bam_standard_staridx-hg19-ensembl_gtf-hg19-ensembl/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24h_10uM.bam' out/ln/alias/sst/all_samples/hg19/bam/Jurkat_PBIT_24h_10uM.bam

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2609
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 2522
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 2319
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, bw_list_id=bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:05 2021]
rule samtools_index:
    input: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.bam
    output: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.bam.bai
    log: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.log
    jobid: 3338
    benchmark: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.benchmark.tsv
    reason: Missing output files: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.bam.bai, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.bam; Input files updated by another job: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.bam
    wildcards: filler=samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3


        (ln -srf out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.bam
        samtools index out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.bam) &> out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.log
        

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2514
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2509
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 2482
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 2633
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2496
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule samtools_index:
    input: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.bam
    output: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.bam.bai
    log: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.log
    jobid: 3337
    benchmark: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.benchmark.tsv
    reason: Missing output files: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.bam.bai, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.bam; Input files updated by another job: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.bam
    wildcards: filler=samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3


        (ln -srf out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.bam
        samtools index out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.bam) &> out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.log
        

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2467
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2528
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2647
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 2511
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2488
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 2269
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2645
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2624
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 2349
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 2652
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2465
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2664
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_bamCoverage_extra:
    input: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam.bai
    output: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw
    log: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 3421
    benchmark: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw; Input files updated by another job: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam.bai
    wildcards: tool=deepTools/bamCoverage, extra=_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM, filler=samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    threads: 2

bamCoverage --bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bam --numberOfProcessors 2  --binSize 20 --minMappingQuality 0 --normalizeUsing RPKM -o out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw &> out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 2661
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 2610
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 2621
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2658
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_bamCoverage_extra:
    input: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam.bai
    output: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw
    log: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 3428
    benchmark: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw; Input files updated by another job: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam.bai, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam
    wildcards: tool=deepTools/bamCoverage, extra=_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM, filler=samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    threads: 2

bamCoverage --bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bam --numberOfProcessors 2  --binSize 20 --minMappingQuality 0 --normalizeUsing RPKM -o out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw &> out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 2339
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, bw_list_id=bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 2250
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-spikein-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 2512
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2524
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2605
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule samtools_index:
    input: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.bam
    output: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.bam.bai
    log: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.log
    jobid: 3339
    benchmark: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.benchmark.tsv
    reason: Missing output files: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.bam.bai; Input files updated by another job: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.bam
    wildcards: filler=samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3


        (ln -srf out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.bam
        samtools index out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.bam) &> out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.log
        

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 2259
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, bw_list_id=bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2505
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2484
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 2470
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 2481
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2518
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 2240
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, bw_list_id=bw-hg19-spikein-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 2521
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule samtools_view_sam_to_bam_extra:
    input: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.sam
    output: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.bam
    log: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.log
    jobid: 3569
    reason: Missing output files: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.bam; Input files updated by another job: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.sam
    wildcards: tool=samtools/view_sam_to_bam, extra=_-q_30, filler=bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3

samtools view -bSh  -q 30 out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.sam -o out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.bam &> out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 2622
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2649
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule gtftk_coverage_extra_chrominfo_bed_bw:
    input: out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_Jurkat.bed, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw
    output: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-sharp_bw-hg19-spikein-h3k4me3-inhibitors.txt
    log: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-sharp_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 26
    reason: Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_Jurkat.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=gtftk/coverage, extra=_-x, chrominfo_id=chrominfo-hg19, bed_list_id=bed-hg19-jurkat-sharp, bw_list_id=bw-hg19-spikein-h3k4me3-inhibitors
    threads: 2


        gtftk coverage  -x --inputfile out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_Jurkat.bed --outputfile out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-sharp_bw-hg19-spikein-h3k4me3-inhibitors.txt --chrom-info out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt --nb-proc 2 out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw &> out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-sharp_bw-hg19-spikein-h3k4me3-inhibitors.log
        

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2469
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 2662
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 2329
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2654
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule samtools_view_sam_to_bam_extra:
    input: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.sam
    output: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.bam
    log: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.log
    jobid: 3558
    reason: Missing output files: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.bam; Input files updated by another job: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.sam
    wildcards: tool=samtools/view_sam_to_bam, extra=_-q_30, filler=bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3

samtools view -bSh  -q 30 out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.sam -o out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.bam &> out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2507
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 2651
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2628
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule samtools_index:
    input: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.bam
    output: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.bam.bai
    log: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.log
    jobid: 3334
    benchmark: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.benchmark.tsv
    reason: Missing output files: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.bam.bai; Input files updated by another job: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.bam
    wildcards: filler=samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3


        (ln -srf out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.bam
        samtools index out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.bam) &> out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.log
        

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 2493
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2636
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2668
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2607
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 2631
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 2513
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_bamCoverage_extra:
    input: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam.bai
    output: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw
    log: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 3426
    benchmark: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw; Input files updated by another job: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam.bai, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam
    wildcards: tool=deepTools/bamCoverage, extra=_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM, filler=samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    threads: 2

bamCoverage --bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bam --numberOfProcessors 2  --binSize 20 --minMappingQuality 0 --normalizeUsing RPKM -o out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw &> out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2475
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule samtools_index:
    input: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.bam
    output: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.bam.bai
    log: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 3434
    benchmark: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.bam.bai, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.bam; Input files updated by another job: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.bam
    wildcards: filler=samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3


        (ln -srf out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.bam
        samtools index out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.bam) &> out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.log
        

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2656
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule samtools_index:
    input: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.bam
    output: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.bam.bai
    log: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 3432
    benchmark: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.bam.bai, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.bam; Input files updated by another job: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.bam
    wildcards: filler=samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3


        (ln -srf out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.bam
        samtools index out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.bam) &> out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.log
        

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 2500
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 2300
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, bw_list_id=bw-hg19-spikein-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 2289
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 2600
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2634
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 2230
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-spikein-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2619
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2526
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 2663
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule samtools_index:
    input: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.bam
    output: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.bam.bai
    log: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.log
    jobid: 3440
    benchmark: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.bam.bai, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.bam; Input files updated by another job: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.bam
    wildcards: filler=samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2


        (ln -srf out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.bam
        samtools index out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.bam) &> out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.log
        

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2498
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2508
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 2623
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2486
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_bamCoverage_extra:
    input: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam.bai
    output: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw
    log: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 3425
    benchmark: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw; Input files updated by another job: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam.bai, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam
    wildcards: tool=deepTools/bamCoverage, extra=_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM, filler=samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    threads: 2

bamCoverage --bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bam --numberOfProcessors 2  --binSize 20 --minMappingQuality 0 --normalizeUsing RPKM -o out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw &> out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 2492
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2477
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 2483
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2626
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_bamCoverage_extra:
    input: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam.bai
    output: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw
    log: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 3422
    benchmark: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw; Input files updated by another job: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam.bai
    wildcards: tool=deepTools/bamCoverage, extra=_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM, filler=samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    threads: 2

bamCoverage --bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bam --numberOfProcessors 2  --binSize 20 --minMappingQuality 0 --normalizeUsing RPKM -o out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw &> out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2479
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 2523
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2666
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2638
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_bamCoverage_extra:
    input: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam.bai
    output: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw
    log: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 3419
    benchmark: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw; Input files updated by another job: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam.bai
    wildcards: tool=deepTools/bamCoverage, extra=_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM, filler=samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    threads: 2

bamCoverage --bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bam --numberOfProcessors 2  --binSize 20 --minMappingQuality 0 --normalizeUsing RPKM -o out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw &> out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 2632
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2617
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 2653
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2615
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2516
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 2491
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 2279
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, bw_list_id=bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 2460
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2494
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 2220
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, bw_list_id=bw-hg19-spikein-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 2640
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 2310
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-spikein-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 2249
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2614
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule samtools_view_sam_to_bam_extra:
    input: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.sam
    output: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.bam
    log: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.log
    jobid: 3559
    reason: Missing output files: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.bam; Input files updated by another job: out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.sam
    wildcards: tool=samtools/view_sam_to_bam, extra=_-q_30, filler=bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2

samtools view -bSh  -q 30 out/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.sam -o out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.bam &> out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:05 2021]
rule samtools_index:
    input: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.bam
    output: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.bam.bai
    log: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 3433
    benchmark: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.bam.bai, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.bam; Input files updated by another job: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.bam
    wildcards: filler=samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3


        (ln -srf out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.bam
        samtools index out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.bam) &> out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.log
        

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 2660
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2495
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule samtools_index:
    input: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.bam
    output: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.bam.bai
    log: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.log
    jobid: 3437
    benchmark: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.bam.bai, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.bam; Input files updated by another job: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.bam
    wildcards: filler=samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3


        (ln -srf out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.bam
        samtools index out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.bam) &> out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.log
        

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 2350
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-spikein-h3k4me3-inhibitors
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 2620
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 2611
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 2270
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-spikein-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 2503
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2646
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 2472
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 2603
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2466
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2497
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 2510
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2639
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2478
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 2320
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, bw_list_id=bw-hg19-spikein-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 2612
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2606
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 2463
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2637
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule samtools_index:
    input: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.bam
    output: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.bam.bai
    log: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.log
    jobid: 3436
    benchmark: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.bam.bai, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.bam; Input files updated by another job: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.bam
    wildcards: filler=samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7


        (ln -srf out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.bam
        samtools index out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.bam) &> out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.log
        

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 2643
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2506
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_bamCoverage_extra:
    input: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam.bai
    output: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    log: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 3420
    benchmark: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw; Input files updated by another job: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam.bai, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam
    wildcards: tool=deepTools/bamCoverage, extra=_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM, filler=samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    threads: 2

bamCoverage --bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bam --numberOfProcessors 2  --binSize 20 --minMappingQuality 0 --normalizeUsing RPKM -o out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw &> out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2499
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 2650
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2618
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 2330
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-spikein-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:05 2021]
rule samtools_index:
    input: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.bam
    output: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.bam.bai
    log: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 3435
    benchmark: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.bam.bai, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.bam; Input files updated by another job: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.bam
    wildcards: filler=samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3


        (ln -srf out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.bam
        samtools index out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.bam) &> out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.log
        

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 2239
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, bw_list_id=bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2474
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 2480
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 2471
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 2260
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, bw_list_id=bw-hg19-spikein-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2635
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 2520
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 2340
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, bw_list_id=bw-hg19-spikein-h3k4me3-inhibitors
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2629
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 2642
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule samtools_index:
    input: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.bam
    output: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.bam.bai
    log: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.log
    jobid: 2354
    benchmark: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.bam.bai; Input files updated by another job: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.bam
    wildcards: filler=samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2


        (ln -srf out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.bam
        samtools index out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.bam) &> out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.log
        

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2669
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 2462
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 2613
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2655
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2476
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2487
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2648
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_bamCoverage_extra:
    input: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam.bai
    output: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw
    log: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 3424
    benchmark: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw; Input files updated by another job: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam.bai
    wildcards: tool=deepTools/bamCoverage, extra=_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM, filler=samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    threads: 2

bamCoverage --bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bam --numberOfProcessors 2  --binSize 20 --minMappingQuality 0 --normalizeUsing RPKM -o out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw &> out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2468
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2527
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 2229
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 2630
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2519
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2604
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2525
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 2290
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-spikein-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 2299
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, bw_list_id=bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2485
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2504
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2657
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 2501
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 2601
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule samtools_index:
    input: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.bam
    output: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.bam.bai
    log: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.log
    jobid: 3438
    benchmark: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.bam.bai; Input files updated by another job: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.bam
    wildcards: filler=samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2


        (ln -srf out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.bam
        samtools index out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.bam) &> out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.log
        

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 2309
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:05 2021]
rule samtools_index:
    input: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.bam
    output: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.bam.bai
    log: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.log
    jobid: 3439
    benchmark: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.bam.bai, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.bam; Input files updated by another job: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.bam
    wildcards: filler=samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI


        (ln -srf out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.bam
        samtools index out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.bam) &> out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.log
        

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2625
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2644
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 2219
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, bw_list_id=bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2659
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 2490
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2665
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2464
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 2280
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, bw_list_id=bw-hg19-spikein-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_bamCoverage_extra:
    input: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam.bai
    output: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw
    log: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 3427
    benchmark: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw; Input files updated by another job: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam.bai, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam
    wildcards: tool=deepTools/bamCoverage, extra=_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM, filler=samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    threads: 2

bamCoverage --bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bam --numberOfProcessors 2  --binSize 20 --minMappingQuality 0 --normalizeUsing RPKM -o out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw &> out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 2461
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2517
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 2641
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2529
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 2602
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 2473
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2515
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 2502
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2489
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2616
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule gtftk_coverage_extra_chrominfo_bed_bw:
    input: out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_Jurkat.bed, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw
    output: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-broad_bw-hg19-spikein-h3k4me3-inhibitors.txt
    log: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-broad_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 28
    reason: Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_Jurkat.bed, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=gtftk/coverage, extra=_-x, chrominfo_id=chrominfo-hg19, bed_list_id=bed-hg19-jurkat-broad, bw_list_id=bw-hg19-spikein-h3k4me3-inhibitors
    threads: 2


        gtftk coverage  -x --inputfile out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_Jurkat.bed --outputfile out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-broad_bw-hg19-spikein-h3k4me3-inhibitors.txt --chrom-info out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt --nb-proc 2 out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw &> out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-broad_bw-hg19-spikein-h3k4me3-inhibitors.log
        

[Sat Apr 17 13:59:05 2021]
rule deepTools_bamCoverage_extra:
    input: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam.bai
    output: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw
    log: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 3423
    benchmark: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw; Input files updated by another job: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam.bai, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam
    wildcards: tool=deepTools/bamCoverage, extra=_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM, filler=samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    threads: 2

bamCoverage --bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bam --numberOfProcessors 2  --binSize 20 --minMappingQuality 0 --normalizeUsing RPKM -o out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw &> out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2667
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2608
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2627
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
localrule ln_alias:
    input: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw
    output: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw
    jobid: 3371
    reason: Missing output files: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw; Input files updated by another job: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw
    wildcards: id=sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw
    priority: 10

ln -srf 'out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw' out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw

[Sat Apr 17 13:59:05 2021]
localrule ln_alias:
    input: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw
    output: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw
    jobid: 3376
    reason: Missing output files: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw; Input files updated by another job: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw
    wildcards: id=sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw
    priority: 10

ln -srf 'out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw' out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw

[Sat Apr 17 13:59:05 2021]
localrule ln_alias:
    input: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw
    output: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw
    jobid: 3370
    reason: Missing output files: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw; Input files updated by another job: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw
    wildcards: id=sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw
    priority: 10

ln -srf 'out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw' out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw

[Sat Apr 17 13:59:05 2021]
localrule ln_alias:
    input: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw
    output: out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw
    jobid: 3374
    reason: Missing output files: out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw; Input files updated by another job: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw
    wildcards: id=sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw
    priority: 10

ln -srf 'out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw' out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw

[Sat Apr 17 13:59:05 2021]
localrule ln_alias:
    input: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw
    output: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw
    jobid: 3373
    reason: Missing output files: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw; Input files updated by another job: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw
    wildcards: id=sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw
    priority: 10

ln -srf 'out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw' out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw

[Sat Apr 17 13:59:05 2021]
localrule ln_alias:
    input: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw
    output: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw
    jobid: 3372
    reason: Missing output files: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw; Input files updated by another job: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw
    wildcards: id=sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw
    priority: 10

ln -srf 'out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw' out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw

[Sat Apr 17 13:59:05 2021]
localrule ln_alias:
    input: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw
    output: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw
    jobid: 3375
    reason: Missing output files: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw; Input files updated by another job: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw
    wildcards: id=sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw
    priority: 10

ln -srf 'out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw' out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw

[Sat Apr 17 13:59:05 2021]
localrule ln_alias:
    input: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw
    output: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw
    jobid: 3367
    reason: Missing output files: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw; Input files updated by another job: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw
    wildcards: id=sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw
    priority: 10

ln -srf 'out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw' out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw

[Sat Apr 17 13:59:05 2021]
localrule ln_alias:
    input: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    output: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw
    jobid: 3368
    reason: Missing output files: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw; Input files updated by another job: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: id=sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw
    priority: 10

ln -srf 'out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw' out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw

[Sat Apr 17 13:59:05 2021]
localrule ln_alias:
    input: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw
    output: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw
    jobid: 3369
    reason: Missing output files: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw; Input files updated by another job: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw
    wildcards: id=sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw
    priority: 10

ln -srf 'out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw' out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw

[Sat Apr 17 13:59:05 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 905
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 158
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:05 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 208
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 462
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_bamCoverage_extra:
    input: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.bam.bai
    output: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.bw
    log: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.log
    jobid: 3390
    benchmark: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.bw; Input files updated by another job: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.bam.bai, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.bam
    wildcards: tool=deepTools/bamCoverage, extra=_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM, filler=samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI
    threads: 2

bamCoverage --bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.bam --numberOfProcessors 2  --binSize 20 --minMappingQuality 0 --normalizeUsing RPKM -o out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.bw &> out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 751
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 198
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_bamCoverage_extra:
    input: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.bam.bai
    output: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.bw
    log: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.log
    jobid: 3388
    benchmark: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.bw; Input files updated by another job: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.bam.bai, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.bam
    wildcards: tool=deepTools/bamCoverage, extra=_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM, filler=samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3
    threads: 2

bamCoverage --bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.bam --numberOfProcessors 2  --binSize 20 --minMappingQuality 0 --normalizeUsing RPKM -o out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.bw &> out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 607
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 589
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 868
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 611
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 139
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 604
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 79
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 767
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 861
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 898
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 754
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 572
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 432
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 119
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 583
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 477
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 900
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 99
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_bamCoverage_extra:
    input: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.bam.bai
    output: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.bw
    log: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.log
    jobid: 2359
    benchmark: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.bw; Input files updated by another job: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.bam.bai, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.bam
    wildcards: tool=deepTools/bamCoverage, extra=_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM, filler=samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3
    threads: 2

bamCoverage --bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.bam --numberOfProcessors 2  --binSize 20 --minMappingQuality 0 --normalizeUsing RPKM -o out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.bw &> out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 745
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 472
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 908
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 628
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 465
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule subread_featureCounts_extra:
    input: out/gtftk/select_by_key_key-gene_biotype_value-protein_coding/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf, out/ln/alias/sst/all_samples/hg19/bam/Jurkat_DMSO_5h.bam, out/ln/alias/sst/all_samples/hg19/bam/Jurkat_PBIT_5h_10uM.bam, out/ln/alias/sst/all_samples/hg19/bam/Jurkat_PBIT_24h_10uM.bam, out/ln/alias/sst/all_samples/hg19/bam/Loucy_DMSO_5h.bam, out/ln/alias/sst/all_samples/hg19/bam/Loucy_PBIT_5h_10uM.bam, out/ln/alias/sst/all_samples/hg19/bam/Loucy_PBIT_24h_10uM.bam
    output: out/subread/featureCounts_-O_gtf-GRCh37-ensembl-r87-protein-coding_bam-hg19-rna-jurkat-loucy-pbit.tsv, out/subread/featureCounts_-O_gtf-GRCh37-ensembl-r87-protein-coding_bam-hg19-rna-jurkat-loucy-pbit.tsv.summary
    log: out/subread/featureCounts_-O_gtf-GRCh37-ensembl-r87-protein-coding_bam-hg19-rna-jurkat-loucy-pbit.log
    jobid: 18
    benchmark: out/subread/featureCounts_-O_gtf-GRCh37-ensembl-r87-protein-coding_bam-hg19-rna-jurkat-loucy-pbit.benchmark.tsv
    reason: Missing output files: out/subread/featureCounts_-O_gtf-GRCh37-ensembl-r87-protein-coding_bam-hg19-rna-jurkat-loucy-pbit.tsv; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bam/Jurkat_DMSO_5h.bam, out/ln/alias/sst/all_samples/hg19/bam/Loucy_PBIT_24h_10uM.bam, out/gtftk/select_by_key_key-gene_biotype_value-protein_coding/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf, out/ln/alias/sst/all_samples/hg19/bam/Jurkat_PBIT_24h_10uM.bam, out/ln/alias/sst/all_samples/hg19/bam/Loucy_DMSO_5h.bam, out/ln/alias/sst/all_samples/hg19/bam/Jurkat_PBIT_5h_10uM.bam, out/ln/alias/sst/all_samples/hg19/bam/Loucy_PBIT_5h_10uM.bam
    wildcards: tool=subread/featureCounts, extra=_-O, gtf_saf_id=gtf-GRCh37-ensembl-r87-protein-coding, bam_list_id=bam-hg19-rna-jurkat-loucy-pbit
    threads: 2

['merge_gene_id_name', 'five_prime_utr', 'gene_id', 'gene_name', 'transcript_id', 'transcript_name']

        featureCounts -a out/gtftk/select_by_key_key-gene_biotype_value-protein_coding/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf  -O -T 2 -o out/subread/featureCounts_-O_gtf-GRCh37-ensembl-r87-protein-coding_bam-hg19-rna-jurkat-loucy-pbit.tsv out/ln/alias/sst/all_samples/hg19/bam/Jurkat_DMSO_5h.bam out/ln/alias/sst/all_samples/hg19/bam/Jurkat_PBIT_5h_10uM.bam out/ln/alias/sst/all_samples/hg19/bam/Jurkat_PBIT_24h_10uM.bam out/ln/alias/sst/all_samples/hg19/bam/Loucy_DMSO_5h.bam out/ln/alias/sst/all_samples/hg19/bam/Loucy_PBIT_5h_10uM.bam out/ln/alias/sst/all_samples/hg19/bam/Loucy_PBIT_24h_10uM.bam &> out/subread/featureCounts_-O_gtf-GRCh37-ensembl-r87-protein-coding_bam-hg19-rna-jurkat-loucy-pbit.log
        

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 752
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 620
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 757
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 239
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 863
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 474
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 259
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 852
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 219
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 712
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 581
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 487
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 618
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 891
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 279
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 884
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 869
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 588
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 58
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 887
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 471
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 742
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 298
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 625
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 68
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 756
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 715
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 866
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 438
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 461
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 569
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 489
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_bamCoverage_extra:
    input: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.bam.bai
    output: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.bw
    log: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 3383
    benchmark: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.bw; Input files updated by another job: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.bam.bai, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.bam
    wildcards: tool=deepTools/bamCoverage, extra=_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM, filler=samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3
    threads: 2

bamCoverage --bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.bam --numberOfProcessors 2  --binSize 20 --minMappingQuality 0 --normalizeUsing RPKM -o out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.bw &> out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 711
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 765
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 574
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 875
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 78
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 238
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 490
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 737
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 249
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 850
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 738
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 482
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 128
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 608
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 763
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 732
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 483
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 888
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 452
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 762
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 268
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 570
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 457
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 458
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 109
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 98
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 218
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 770
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 854
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 595
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 485
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 431
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 769
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 718
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 741
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 586
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 849
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 476
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_bamCoverage_extra:
    input: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.bam.bai
    output: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.bw
    log: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 3386
    benchmark: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.bw; Input files updated by another job: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.bam.bai, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.bam
    wildcards: tool=deepTools/bamCoverage, extra=_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM, filler=samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3
    threads: 2

bamCoverage --bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.bam --numberOfProcessors 2  --binSize 20 --minMappingQuality 0 --normalizeUsing RPKM -o out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.bw &> out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 435
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 428
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_bamCoverage_extra:
    input: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.bam.bai
    output: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.bw
    log: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.log
    jobid: 3389
    benchmark: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.bw; Input files updated by another job: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.bam.bai
    wildcards: tool=deepTools/bamCoverage, extra=_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM, filler=samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2
    threads: 2

bamCoverage --bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.bam --numberOfProcessors 2  --binSize 20 --minMappingQuality 0 --normalizeUsing RPKM -o out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.bw &> out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 768
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 733
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 912
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 871
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 901
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 910
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 723
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 622
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 603
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 423
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 479
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 870
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 759
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 590
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 703
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 883
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 902
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 443
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 621
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 632
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 591
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 630
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 453
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 488
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 708
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 580
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 451
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 760
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 612
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 69
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 450
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_bamCoverage_extra:
    input: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.bam.bai
    output: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.bw
    log: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.log
    jobid: 2357
    benchmark: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.bw; Input files updated by another job: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.bam.bai, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.bam
    wildcards: tool=deepTools/bamCoverage, extra=_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM, filler=samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3
    threads: 2

bamCoverage --bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.bam --numberOfProcessors 2  --binSize 20 --minMappingQuality 0 --normalizeUsing RPKM -o out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.bw &> out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 894
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 573
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 629
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 874
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 587
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 439
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 707
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 199
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 434
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 713
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 714
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 59
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 433
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 427
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 719
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 867
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 594
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 909
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule subread_featureCounts_extra:
    input: out/gtftk/select_by_key_key-gene_biotype_value-protein_coding/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf, out/ln/alias/sst/all_samples/hg19/bam/Jurkat_DMSO_5h.bam, out/ln/alias/sst/all_samples/hg19/bam/Loucy_DMSO_5h.bam
    output: out/subread/featureCounts_-O_gtf-GRCh37-ensembl-r87-protein-coding_bam-hg19-rna-jurkat-loucy.tsv, out/subread/featureCounts_-O_gtf-GRCh37-ensembl-r87-protein-coding_bam-hg19-rna-jurkat-loucy.tsv.summary
    log: out/subread/featureCounts_-O_gtf-GRCh37-ensembl-r87-protein-coding_bam-hg19-rna-jurkat-loucy.log
    jobid: 21
    benchmark: out/subread/featureCounts_-O_gtf-GRCh37-ensembl-r87-protein-coding_bam-hg19-rna-jurkat-loucy.benchmark.tsv
    reason: Missing output files: out/subread/featureCounts_-O_gtf-GRCh37-ensembl-r87-protein-coding_bam-hg19-rna-jurkat-loucy.tsv; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bam/Loucy_DMSO_5h.bam, out/gtftk/select_by_key_key-gene_biotype_value-protein_coding/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf, out/ln/alias/sst/all_samples/hg19/bam/Jurkat_DMSO_5h.bam
    wildcards: tool=subread/featureCounts, extra=_-O, gtf_saf_id=gtf-GRCh37-ensembl-r87-protein-coding, bam_list_id=bam-hg19-rna-jurkat-loucy
    threads: 2

['merge_gene_id_name', 'five_prime_utr', 'gene_id', 'gene_name', 'transcript_id', 'transcript_name']

        featureCounts -a out/gtftk/select_by_key_key-gene_biotype_value-protein_coding/gunzip/to-stdout/wget/ftp/ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf  -O -T 2 -o out/subread/featureCounts_-O_gtf-GRCh37-ensembl-r87-protein-coding_bam-hg19-rna-jurkat-loucy.tsv out/ln/alias/sst/all_samples/hg19/bam/Jurkat_DMSO_5h.bam out/ln/alias/sst/all_samples/hg19/bam/Loucy_DMSO_5h.bam &> out/subread/featureCounts_-O_gtf-GRCh37-ensembl-r87-protein-coding_bam-hg19-rna-jurkat-loucy.log
        

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 853
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 614
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_bamCoverage_extra:
    input: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.bam.bai
    output: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.bw
    log: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.log
    jobid: 3391
    benchmark: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.bw; Input files updated by another job: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.bam.bai, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.bam
    wildcards: tool=deepTools/bamCoverage, extra=_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM, filler=samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2
    threads: 2

bamCoverage --bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.bam --numberOfProcessors 2  --binSize 20 --minMappingQuality 0 --normalizeUsing RPKM -o out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.bw &> out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 209
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_bamCoverage_extra:
    input: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.bam.bai
    output: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.bw
    log: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.log
    jobid: 3387
    benchmark: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.bw; Input files updated by another job: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.bam.bai, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.bam
    wildcards: tool=deepTools/bamCoverage, extra=_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM, filler=samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7
    threads: 2

bamCoverage --bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.bam --numberOfProcessors 2  --binSize 20 --minMappingQuality 0 --normalizeUsing RPKM -o out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.bw &> out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 730
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 892
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 731
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 480
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_bamCoverage_extra:
    input: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.bam.bai
    output: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.bw
    log: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 3384
    benchmark: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.bw; Input files updated by another job: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.bam.bai, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.bam
    wildcards: tool=deepTools/bamCoverage, extra=_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM, filler=samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3
    threads: 2

bamCoverage --bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.bam --numberOfProcessors 2  --binSize 20 --minMappingQuality 0 --normalizeUsing RPKM -o out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.bw &> out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 860
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 605
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 865
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 726
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 299
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 864
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 129
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 878
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 876
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 710
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 706
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 729
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 436
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 619
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 484
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 468
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 747
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 288
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 724
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 289
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_bamCoverage_extra:
    input: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.bam.bai
    output: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.bw
    log: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.log
    jobid: 2353
    benchmark: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.bw; Input files updated by another job: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.bam.bai
    wildcards: tool=deepTools/bamCoverage, extra=_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM, filler=samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3
    threads: 2

bamCoverage --bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.bam --numberOfProcessors 2  --binSize 20 --minMappingQuality 0 --normalizeUsing RPKM -o out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.bw &> out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 491
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 843
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 571
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 851
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 563
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 771
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 444
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 149
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 148
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 899
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 467
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 748
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 764
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 449
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 716
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 426
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 278
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 430
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 596
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 584
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 269
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 159
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 446
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 598
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 585
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 885
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_bamCoverage_extra:
    input: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.bam.bai
    output: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.bw
    log: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.log
    jobid: 325
    benchmark: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.bw; Input files updated by another job: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.bam.bai
    wildcards: tool=deepTools/bamCoverage, extra=_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM, filler=samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2
    threads: 2

bamCoverage --bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.bam --numberOfProcessors 2  --binSize 20 --minMappingQuality 0 --normalizeUsing RPKM -o out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.bw &> out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 740
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 168
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 481
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 582
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:06 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 258
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 473
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 441
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 855
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 873
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 844
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 728
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 889
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 890
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 486
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 746
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 615
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 704
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 178
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 469
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 906
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 617
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 859
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 576
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 169
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 848
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 179
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:07 2021]
rule samtools_sort_extra:
    input: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.bam
    output: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.bam
    log: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.log
    jobid: 3504
    reason: Missing output files: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.bam; Input files updated by another job: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.bam
    wildcards: tool=samtools/sort, extra=, filler=samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3
    threads: 2

samtools sort -@ 2 -T out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.bam  out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.bam -o out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.bam &> out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 88
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 228
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 319
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 568
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 309
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 579
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 897
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 856
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 626
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 749
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 318
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 895
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 424
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 609
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 610
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 766
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 466
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 448
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 564
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 753
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 593
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 118
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 862
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 721
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 575
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 138
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 460
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 761
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 308
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 877
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 456
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 758
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 845
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 904
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 623
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 429
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 601
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 872
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 459
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_bamCoverage_extra:
    input: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.bam.bai
    output: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.bw
    log: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 3385
    benchmark: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.bw; Input files updated by another job: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.bam.bai, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.bam
    wildcards: tool=deepTools/bamCoverage, extra=_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM, filler=samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3
    threads: 2

bamCoverage --bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.bam --numberOfProcessors 2  --binSize 20 --minMappingQuality 0 --normalizeUsing RPKM -o out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.bw &> out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 616
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 49
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 445
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 720
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 847
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 442
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 727
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 492
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 600
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 606
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 880
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 886
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 447
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 772
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 567
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 722
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 440
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 896
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 189
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 725
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 739
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 709
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 881
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 592
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 903
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 565
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 624
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule samtools_sort_extra:
    input: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.bam
    output: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.bam
    log: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.log
    jobid: 3493
    reason: Missing output files: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.bam; Input files updated by another job: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.bam
    wildcards: tool=samtools/sort, extra=, filler=samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3
    threads: 2

samtools sort -@ 2 -T out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.bam  out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.bam -o out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.bam &> out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 478
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 597
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 736
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 475
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 631
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 108
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 857
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 454
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 846
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 602
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 907
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 229
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 613
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 425
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 464
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 717
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 48
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 750
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 858
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 599
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 735
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 743
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_bamCoverage_extra:
    input: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.bam.bai
    output: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.bw
    log: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.log
    jobid: 2361
    benchmark: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.bw; Input files updated by another job: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.bam.bai
    wildcards: tool=deepTools/bamCoverage, extra=_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM, filler=samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3
    threads: 2

bamCoverage --bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.bam --numberOfProcessors 2  --binSize 20 --minMappingQuality 0 --normalizeUsing RPKM -o out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.bw &> out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 463
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 879
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 455
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 470
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 578
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 893
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 437
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 705
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 744
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 188
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 882
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 627
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 89
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:07 2021]
rule samtools_sort_extra:
    input: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.bam
    output: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.bam
    log: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.log
    jobid: 3494
    reason: Missing output files: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.bam; Input files updated by another job: out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.bam
    wildcards: tool=samtools/sort, extra=, filler=samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2
    threads: 2

samtools sort -@ 2 -T out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.bam  out/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.bam -o out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.bam &> out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 248
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 577
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 734
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 566
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 755
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 911
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
localrule ln_alias:
    input: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.bw
    output: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw
    jobid: 3325
    reason: Missing output files: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw; Input files updated by another job: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.bw
    wildcards: id=sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw
    priority: 10

ln -srf 'out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536556_H3K4me3.bw' out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw

[Sat Apr 17 13:59:07 2021]
localrule ln_alias:
    input: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.bw
    output: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw
    jobid: 3327
    reason: Missing output files: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw; Input files updated by another job: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.bw
    wildcards: id=sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw
    priority: 10

ln -srf 'out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1057275_CDK7.bw' out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw

[Sat Apr 17 13:59:07 2021]
localrule ln_alias:
    input: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.bw
    output: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw
    jobid: 3323
    reason: Missing output files: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw; Input files updated by another job: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.bw
    wildcards: id=sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw
    priority: 10

ln -srf 'out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536543_H3K4me3.bw' out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw

[Sat Apr 17 13:59:07 2021]
localrule ln_alias:
    input: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.bw
    output: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw
    jobid: 3331
    reason: Missing output files: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw; Input files updated by another job: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.bw
    wildcards: id=sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw
    priority: 10

ln -srf 'out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR231122_DNaseI.bw' out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw

[Sat Apr 17 13:59:07 2021]
localrule ln_alias:
    input: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.bw
    output: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw
    jobid: 3330
    reason: Missing output files: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw; Input files updated by another job: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.bw
    wildcards: id=sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw
    priority: 10

ln -srf 'out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.bw' out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw

[Sat Apr 17 13:59:07 2021]
localrule ln_alias:
    input: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.bw
    output: out/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.bw
    jobid: 324
    reason: Missing output files: out/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.bw; Input files updated by another job: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.bw
    wildcards: id=sst/all_samples/hg19/bw/TH91_EC_H3K4me3.bw
    priority: 10

ln -srf 'out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_EC_H3K4me3.bw' out/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.bw

[Sat Apr 17 13:59:07 2021]
localrule ln_alias:
    input: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.bw
    output: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw
    jobid: 3328
    reason: Missing output files: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw; Input files updated by another job: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.bw
    wildcards: id=sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw
    priority: 10

ln -srf 'out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR11783980_H3K36me3.bw' out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw

[Sat Apr 17 13:59:07 2021]
localrule ln_alias:
    input: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.bw
    output: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw
    jobid: 3324
    reason: Missing output files: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw; Input files updated by another job: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.bw
    wildcards: id=sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw
    priority: 10

ln -srf 'out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_Ctrl_SRR1536552_H3K4me3.bw' out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw

[Sat Apr 17 13:59:07 2021]
localrule ln_alias:
    input: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.bw
    output: out/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.bw
    jobid: 330
    reason: Missing output files: out/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.bw; Input files updated by another job: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.bw
    wildcards: id=sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.bw
    priority: 10

ln -srf 'out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP4_H3K4me3.bw' out/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.bw

[Sat Apr 17 13:59:07 2021]
localrule ln_alias:
    input: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.bw
    output: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    jobid: 3329
    reason: Missing output files: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw; Input files updated by another job: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.bw
    wildcards: id=sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    priority: 10

ln -srf 'out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR1536561_H3K79me2.bw' out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw

[Sat Apr 17 13:59:07 2021]
localrule ln_alias:
    input: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.bw
    output: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw
    jobid: 3326
    reason: Missing output files: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw; Input files updated by another job: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.bw
    wildcards: id=sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw
    priority: 10

ln -srf 'out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_EPZ_SRR1536572_H3K4me3.bw' out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw

[Sat Apr 17 13:59:07 2021]
localrule ln_alias:
    input: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.bw
    output: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw
    jobid: 3332
    reason: Missing output files: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw; Input files updated by another job: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.bw
    wildcards: id=sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw
    priority: 10

ln -srf 'out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRR5338727_H3K79me2.bw' out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw

[Sat Apr 17 13:59:07 2021]
localrule ln_alias:
    input: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.bw
    output: out/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.bw
    jobid: 332
    reason: Missing output files: out/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.bw; Input files updated by another job: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.bw
    wildcards: id=sst/all_samples/hg19/bw/TH91_LC_H3K4me3.bw
    priority: 10

ln -srf 'out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_LC_H3K4me3.bw' out/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.bw

[Sat Apr 17 13:59:07 2021]
localrule ln_alias:
    input: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.bw
    output: out/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.bw
    jobid: 328
    reason: Missing output files: out/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.bw; Input files updated by another job: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.bw
    wildcards: id=sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.bw
    priority: 10

ln -srf 'out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/TH91_SP8_H3K4me3.bw' out/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.bw

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2803
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule r_extract_control_sharp_subsets_from_our_rnaseq:
    input: out/subread/featureCounts_-O_gtf-GRCh37-ensembl-r87-protein-coding_bam-hg19-rna-jurkat-loucy.tsv, out/sort/_-u_-k1,1_-k2,2n/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_Jurkat.bed, out/sort/_-u_-k1,1_-k2,2n/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_Jurkat.bed
    output: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Sharp.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Sharp_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp_trim_500b_at_TSS_TES.bed
    jobid: 9
    reason: Missing output files: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Sharp.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed; Input files updated by another job: out/sort/_-u_-k1,1_-k2,2n/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_Jurkat.bed, out/sort/_-u_-k1,1_-k2,2n/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_Jurkat.bed, out/subread/featureCounts_-O_gtf-GRCh37-ensembl-r87-protein-coding_bam-hg19-rna-jurkat-loucy.tsv

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 2932
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 3254
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 3219
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2714
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2715
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 2839
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 2838
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 3115
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 3114
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 3079
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 3218
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2756
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 3205
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 2978
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2758
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 2745
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 3216
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 3263
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 2885
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 2884
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2941
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 3299
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 3298
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 2794
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2759
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2987
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 3175
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 3070
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 3174
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 3023
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 3022
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2943
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2802
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 2975
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2988
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 3129
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 3208
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 3128
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 3265
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2942
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 2929
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2853
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2852
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 2701
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 2700
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2989
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2757
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 3078
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 3264
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 3251
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 3217
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 3080
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 3067
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 3036
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 3037
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 3262
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2805
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2940
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 3161
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 3160
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 3312
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 3313
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2986
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 3081
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 2748
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2804
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 2791
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2898
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2899
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2761
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2760
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 2793
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 2792
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 3300
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 3173
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 2886
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2849
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 3024
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 3172
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 3125
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2710
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 3159
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 3069
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:07 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 3068
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 2840
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule r_compute_pausing_index:
    input: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/r/compute_pausing_index/pi_boxplot.pdf, out/r/compute_pausing_index/pi_boxplot.png
    jobid: 7
    reason: Missing output files: out/r/compute_pausing_index/pi_boxplot.png; Input files updated by another job: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2895
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 3253
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 3252
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 3309
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 2931
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 2930
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2712
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 2699
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 3170
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 2977
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 2976
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 3220
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 3221
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 3116
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 3033
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2713
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 3082
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 3083
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 3162
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 3311
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 3021
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 3034
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2897
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2848
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 3310
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 3297
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2711
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 3035
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 3124
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2806
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2807
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 2747
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 2746
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule samtools_index:
    input: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.bam
    output: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.bam.bai
    log: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.log
    jobid: 3441
    benchmark: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.bam.bai, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.bam; Input files updated by another job: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.bam
    wildcards: filler=samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3


        (ln -srf out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.bam
        samtools index out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.bam) &> out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.log
        

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2896
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule samtools_index:
    input: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.bam
    output: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.bam.bai
    log: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.log
    jobid: 3431
    benchmark: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.bam.bai; Input files updated by another job: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.bam
    wildcards: filler=samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2


        (ln -srf out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.bam
        samtools index out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.bam) &> out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.log
        

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 2883
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 3207
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 3206
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2851
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2894
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2991
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 3308
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2990
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 3126
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 3171
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 3113
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2945
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2944
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2850
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 2837
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule samtools_index:
    input: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.bam
    output: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.bam.bai
    log: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.log
    jobid: 3430
    benchmark: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.bam.bai, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.bam; Input files updated by another job: out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.bam
    wildcards: filler=samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3


        (ln -srf out/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.bam
        samtools index out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.bam) &> out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.log
        

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 2702
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 3267
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 3032
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 3266
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 3127
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1313
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1635
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1462
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1186
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 3017
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 2811
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1862
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 2334
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, bw_list_id=bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 3030
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1404
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1786
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1459
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 3233
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 3236
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2103
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1142
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 2048
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 3290
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2585
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 2949
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 3025
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1218
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 3167
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 3111
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 3164
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 3059
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 3139
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2106
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1830
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 991
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2534
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1957
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1586
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 3306
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1128
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 2580
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 2751
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:08 2021]
rule gtftk_coverage_extra_chrominfo_bed_bw:
    input: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Sharp2.bed, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.bw, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.bw, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.bw, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.bw
    output: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-sharp2-from-our-rnaseq-subsets_bw-hg19-Orlando2014-Jurkat.txt
    log: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-sharp2-from-our-rnaseq-subsets_bw-hg19-Orlando2014-Jurkat.log
    jobid: 1
    reason: Missing output files: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-sharp2-from-our-rnaseq-subsets_bw-hg19-Orlando2014-Jurkat.txt; Input files updated by another job: out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.bw, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.bw, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.bw, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.bw, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Sharp2.bed
    wildcards: tool=gtftk/coverage, extra=_-x, chrominfo_id=chrominfo-hg19, bed_list_id=bed-hg19-jurkat-sharp2-from-our-rnaseq-subsets, bw_list_id=bw-hg19-Orlando2014-Jurkat
    threads: 2


        gtftk coverage  -x --inputfile out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Sharp2.bed --outputfile out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-sharp2-from-our-rnaseq-subsets_bw-hg19-Orlando2014-Jurkat.txt --chrom-info out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt --nb-proc 2 out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.bw out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.bw out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.bw out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.bw &> out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-sharp2-from-our-rnaseq-subsets_bw-hg19-Orlando2014-Jurkat.log
        

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2873
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 2887
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 2844
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 2274
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, bw_list_id=bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 2860
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 3293
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 955
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2784
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1553
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 2822
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1828
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 2819
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1000
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 2721
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2688
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 2879
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1644
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 3156
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1184
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2197
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 2244
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1599
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 2892
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 3014
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 3225
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 3301
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 2295
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, bw_list_id=bw-hg19-spikein-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 2957
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 2960
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1772
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 942
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1280
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2149
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 2234
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, bw_list_id=bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 3028
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2734
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 3006
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 2305
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-spikein-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 3003
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 3271
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2968
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1450
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2062
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1418
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 2906
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 2094
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 2284
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2919
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 2440
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 2675
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 3066
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 2773
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 2776
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2830
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1505
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1924
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 2995
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 3244
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2445
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1358
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 2833
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 3282
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1277
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1324
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 3279
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1278
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2394
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 2846
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1600
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 3185
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1877
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 3105
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 3304
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 2841
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 2765
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1233
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 956
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1922
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 2890
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1968
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1921
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 2002
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 2344
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1046
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1601
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2107
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule gtftk_coverage_extra_chrominfo_bed_bw:
    input: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Sharp1.bed, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.bw, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.bw, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.bw, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.bw
    output: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-sharp1-from-our-rnaseq-subsets_bw-hg19-Orlando2014-Jurkat.txt
    log: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-sharp1-from-our-rnaseq-subsets_bw-hg19-Orlando2014-Jurkat.log
    jobid: 3
    reason: Missing output files: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-sharp1-from-our-rnaseq-subsets_bw-hg19-Orlando2014-Jurkat.txt; Input files updated by another job: out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.bw, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.bw, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.bw, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Sharp1.bed
    wildcards: tool=gtftk/coverage, extra=_-x, chrominfo_id=chrominfo-hg19, bed_list_id=bed-hg19-jurkat-sharp1-from-our-rnaseq-subsets, bw_list_id=bw-hg19-Orlando2014-Jurkat
    threads: 2


        gtftk coverage  -x --inputfile out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Sharp1.bed --outputfile out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-sharp1-from-our-rnaseq-subsets_bw-hg19-Orlando2014-Jurkat.txt --chrom-info out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt --nb-proc 2 out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.bw out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.bw out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.bw out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.bw &> out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-sharp1-from-our-rnaseq-subsets_bw-hg19-Orlando2014-Jurkat.log
        

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1266
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 2571
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2437
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2555
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1873
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 2818
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 2948
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 2863
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 2891
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 2888
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1036
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 2999
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1095
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 2961
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2736
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1739
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 3305
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1680
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 3302
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 2956
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 3018
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 2810
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule gtftk_coverage_extra_chrominfo_bed_bw:
    input: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Sharp3.bed, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.bw, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.bw, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.bw, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.bw
    output: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-sharp3-from-our-rnaseq-subsets_bw-hg19-Orlando2014-Jurkat.txt
    log: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-sharp3-from-our-rnaseq-subsets_bw-hg19-Orlando2014-Jurkat.log
    jobid: 22
    reason: Missing output files: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-sharp3-from-our-rnaseq-subsets_bw-hg19-Orlando2014-Jurkat.txt; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Sharp3.bed, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.bw, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.bw, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.bw, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.bw, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt
    wildcards: tool=gtftk/coverage, extra=_-x, chrominfo_id=chrominfo-hg19, bed_list_id=bed-hg19-jurkat-sharp3-from-our-rnaseq-subsets, bw_list_id=bw-hg19-Orlando2014-Jurkat
    threads: 2


        gtftk coverage  -x --inputfile out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Sharp3.bed --outputfile out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-sharp3-from-our-rnaseq-subsets_bw-hg19-Orlando2014-Jurkat.txt --chrom-info out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt --nb-proc 2 out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.bw out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.bw out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.bw out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.bw &> out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-sharp3-from-our-rnaseq-subsets_bw-hg19-Orlando2014-Jurkat.log
        

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 2452
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 3042
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1229
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 3281
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 2697
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2439
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1910
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2458
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 2769
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 957
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 2823
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1463
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1690
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 2880
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 3275
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2548
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 2682
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:08 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 3073
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 3155
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 3237
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 2542
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 2573
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 2775
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2013
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 3224
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 3168
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 3046
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2428
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 3149
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 3163
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 2550
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 3136
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2687
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 2422
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 3005
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1369
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 3232
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 3294
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2576
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 3029
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 3026
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 2959
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2061
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 2562
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 3182
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2733
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 2410
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1691
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2568
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 3195
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1597
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2436
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 3278
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1727
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1694
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1139
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1050
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1083
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1783
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 2433
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 2821
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 2402
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 3283
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 953
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 2728
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 3229
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2408
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 2845
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1047
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 2842
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 3092
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 2744
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1417
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 3270
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 2764
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 3002
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:09 2021]
rule gtftk_coverage_extra_chrominfo_bed_single_bw:
    input: out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_EC_TH91_H3K4me3_S010NDH1.bed, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.bw
    output: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-ec-broad/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.txt
    log: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-ec-broad/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.log
    jobid: 6
    reason: Missing output files: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-ec-broad/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.txt; Input files updated by another job: out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.bw, out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_EC_TH91_H3K4me3_S010NDH1.bed
    wildcards: tool=gtftk/coverage, extra=_-x, chrominfo_id=chrominfo-hg19, bed_list_id=bed-hg19-ec-broad, filler=ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3
    threads: 2


        gtftk coverage  -x --inputfile out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_EC_TH91_H3K4me3_S010NDH1.bed --outputfile out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-ec-broad/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.txt --chrom-info out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt --nb-proc 2 out/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.bw &> out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-ec-broad/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.log
        

[Sat Apr 17 13:59:09 2021]
rule gtftk_coverage_extra_chrominfo_bed_single_bw:
    input: out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD8_TH91_H3K4me3_S010S3H1.bed, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.bw
    output: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-cd8-sharp/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.txt
    log: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-cd8-sharp/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.log
    jobid: 8
    reason: Missing output files: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-cd8-sharp/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.txt; Input files updated by another job: out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD8_TH91_H3K4me3_S010S3H1.bed, out/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.bw
    wildcards: tool=gtftk/coverage, extra=_-x, chrominfo_id=chrominfo-hg19, bed_list_id=bed-hg19-cd8-sharp, filler=ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3
    threads: 2


        gtftk coverage  -x --inputfile out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD8_TH91_H3K4me3_S010S3H1.bed --outputfile out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-cd8-sharp/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.txt --chrom-info out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt --nb-proc 2 out/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.bw &> out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-cd8-sharp/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.log
        

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1415
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 3166
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1555
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2690
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1510
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1726
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1966
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 2777
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 943
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2598
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 2815
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 3235
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1325
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2579
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 3088
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 2592
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 2994
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 2834
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 2772
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2577
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2415
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1969
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 2431
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1587
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.bw, out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_EC_TH91_H3K4me3_S010NDH1.bed, out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_EC_TH91_H3K4me3_S010NDH1.bed
    output: out/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-ec-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-ec-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.log
    jobid: 2207
    benchmark: out/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-ec-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-ec-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.txt.gz; Input files updated by another job: out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_EC_TH91_H3K4me3_S010NDH1.bed, out/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.bw, out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_EC_TH91_H3K4me3_S010NDH1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_--referencePoint_center_-b_5000_-a_5000, bed_list_id=bed-hg19-ec-sharp-broad, filler=ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3
    threads: 2

computeMatrix  reference-point --referencePoint center -b 5000 -a 5000 --regionsFileName out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_EC_TH91_H3K4me3_S010NDH1.bed out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_EC_TH91_H3K4me3_S010NDH1.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-ec-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-ec-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2154
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1082
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 3007
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1322
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 2953
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2199
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2059
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 2909
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2195
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1919
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1461
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 3242
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2589
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 3180
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 2139
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2538
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 2774
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 2532
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 3009
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 2683
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1219
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 3074
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1863
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_bamCoverage_extra:
    input: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.bam.bai
    output: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.bw
    log: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.log
    jobid: 3381
    benchmark: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.bw; Input files updated by another job: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.bam.bai, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.bam
    wildcards: tool=deepTools/bamCoverage, extra=_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM, filler=samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3
    threads: 2

bamCoverage --bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.bam --numberOfProcessors 2  --binSize 20 --minMappingQuality 0 --normalizeUsing RPKM -o out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.bw &> out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 3020
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2921
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1495
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2587
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 3004
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2779
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2105
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1275
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 2441
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1551
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2446
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 2882
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 3285
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2966
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 3090
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 2726
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 3103
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 3184
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 2265
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-spikein-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 2789
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 2677
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 2731
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 3280
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2828
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 3296
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 2443
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 2718
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 3076
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 3234
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 2685
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1402
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 2723
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 2255
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, bw_list_id=bw-hg19-spikein-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 3138
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 2672
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 3063
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 3165
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1770
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 2583
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_bamCoverage_extra:
    input: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.bam.bai
    output: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.bw
    log: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.log
    jobid: 3382
    benchmark: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.bw; Input files updated by another job: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.bam.bai
    wildcards: tool=deepTools/bamCoverage, extra=_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM, filler=samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2
    threads: 2

bamCoverage --bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.bam --numberOfProcessors 2  --binSize 20 --minMappingQuality 0 --normalizeUsing RPKM -o out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.bw &> out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.bw, out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD8_TH91_H3K4me3_S010S3H1.bed, out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD8_TH91_H3K4me3_S010S3H1.bed
    output: out/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-cd8-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-cd8-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.log
    jobid: 322
    benchmark: out/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-cd8-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-cd8-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.txt.gz; Input files updated by another job: out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD8_TH91_H3K4me3_S010S3H1.bed, out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD8_TH91_H3K4me3_S010S3H1.bed, out/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_--referencePoint_center_-b_5000_-a_5000, bed_list_id=bed-hg19-cd8-sharp-broad, filler=ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3
    threads: 2

computeMatrix  reference-point --referencePoint center -b 5000 -a 5000 --regionsFileName out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD8_TH91_H3K4me3_S010S3H1.bed out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD8_TH91_H3K4me3_S010S3H1.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-cd8-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-cd8-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1321
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2782
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1965
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1126
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 2973
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 3239
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2586
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 2680
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 2742
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 3057
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 3071
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 2046
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 3012
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 3044
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 2927
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2875
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1371
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1692
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1091
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 2581
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2825
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 2958
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2447
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 2001
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1602
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1357
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 2753
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 2750
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 3134
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2449
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 958
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 3288
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 2836
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1735
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 2729
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 3249
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2963
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1048
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 2392
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 2820
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2015
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_bamCoverage_extra:
    input: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.bam, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.bam.bai
    output: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.bw
    log: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.log
    jobid: 3392
    benchmark: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.bw; Input files updated by another job: out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.bam.bai, out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.bam
    wildcards: tool=deepTools/bamCoverage, extra=_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM, filler=samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3
    threads: 2

bamCoverage --bam out/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.bam --numberOfProcessors 2  --binSize 20 --minMappingQuality 0 --normalizeUsing RPKM -o out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.bw &> out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2398
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1234
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1817
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2692
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 2730
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 3197
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 2727
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 2813
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.bw, out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD4_TH91_H3K4me3_S010R5H1.bed, out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD4_TH91_H3K4me3_S010R5H1.bed
    output: out/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-cd4-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-cd4-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.log
    jobid: 345
    benchmark: out/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-cd4-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-cd4-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.bw, out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD4_TH91_H3K4me3_S010R5H1.bed, out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD4_TH91_H3K4me3_S010R5H1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_--referencePoint_center_-b_5000_-a_5000, bed_list_id=bed-hg19-cd4-sharp-broad, filler=ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3
    threads: 2

computeMatrix  reference-point --referencePoint center -b 5000 -a 5000 --regionsFileName out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD4_TH91_H3K4me3_S010R5H1.bed out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD4_TH91_H3K4me3_S010R5H1.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-cd4-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-cd4-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 3093
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2454
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 3010
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 2843
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2104
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2435
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2557
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 2411
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 2752
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2559
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 2904
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 2951
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1460
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2780
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 2224
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1173
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1878
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 2186
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 2325
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-spikein-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:09 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 2908
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2424
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 3286
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2014
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1541
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1771
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 2413
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 2719
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2416
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 3158
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2544
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1127
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 2185
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 3227
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1370
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 2430
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1542
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 2754
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2404
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 3303
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2556
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 2095
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1509
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 2570
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2058
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 2741
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 3273
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2060
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1035
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1679
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 3240
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1416
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2564
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 2862
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1414
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 2315
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, bw_list_id=bw-hg19-spikein-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2153
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1451
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 3064
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 2673
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 2749
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 2889
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 2553
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 2997
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 2858
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 2047
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1267
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2419
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1080
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1738
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1643
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1689
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 344
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, bw_list_id=bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:10 2021]
rule gtftk_coverage_extra_chrominfo_bed_bw:
    input: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Broad.bed, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw
    output: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-broad-from-our-rnaseq-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt
    log: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-broad-from-our-rnaseq-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 14
    reason: Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Broad.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=gtftk/coverage, extra=_-x, chrominfo_id=chrominfo-hg19, bed_list_id=bed-hg19-jurkat-broad-from-our-rnaseq-subsets, bw_list_id=bw-hg19-spikein-h3k4me3-inhibitors
    threads: 2


        gtftk coverage  -x --inputfile out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Broad.bed --outputfile out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-broad-from-our-rnaseq-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt --chrom-info out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt --nb-proc 2 out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw &> out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-broad-from-our-rnaseq-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
        

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1187
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1185
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 3027
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2826
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 2767
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 3047
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1829
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 2681
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 3075
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 3072
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 3203
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 2684
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 3151
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1831
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2738
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1045
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 999
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1094
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 2551
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2575
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2417
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1911
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1724
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1403
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2964
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2594
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1310
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 989
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1464
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 2304
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1221
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2874
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1923
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule gtftk_coverage_extra_chrominfo_bed_single_bw:
    input: out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_LC_TH91_H3K4me3_S010Q7H1.bed, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.bw
    output: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-lc-sharp/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.txt
    log: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-lc-sharp/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.log
    jobid: 11
    reason: Missing output files: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-lc-sharp/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.txt; Input files updated by another job: out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.bw, out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_LC_TH91_H3K4me3_S010Q7H1.bed
    wildcards: tool=gtftk/coverage, extra=_-x, chrominfo_id=chrominfo-hg19, bed_list_id=bed-hg19-lc-sharp, filler=ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3
    threads: 2


        gtftk coverage  -x --inputfile out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_LC_TH91_H3K4me3_S010Q7H1.bed --outputfile out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-lc-sharp/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.txt --chrom-info out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt --nb-proc 2 out/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.bw &> out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-lc-sharp/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.log
        

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 2235
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, bw_list_id=bw-hg19-spikein-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 2974
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2395
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 3289
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 3120
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1279
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2444
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1865
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2108
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 3060
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 3098
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1954
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1633
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 2285
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-spikein-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 3095
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 2725
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 3250
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2917
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 2390
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1955
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1864
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 2835
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2783
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1784
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 3135
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 2003
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1496
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 2140
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 2345
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-spikein-h3k4me3-inhibitors
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:10 2021]
rule gtftk_coverage_extra_chrominfo_bed_bw:
    input: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Broad.bed, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.bw, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.bw, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.bw, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.bw
    output: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-broad-from-our-rnaseq-subsets_bw-hg19-Orlando2014-Jurkat.txt
    log: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-broad-from-our-rnaseq-subsets_bw-hg19-Orlando2014-Jurkat.log
    jobid: 19
    reason: Missing output files: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-broad-from-our-rnaseq-subsets_bw-hg19-Orlando2014-Jurkat.txt; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Broad.bed, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.bw, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.bw, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.bw, out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.bw, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt
    wildcards: tool=gtftk/coverage, extra=_-x, chrominfo_id=chrominfo-hg19, bed_list_id=bed-hg19-jurkat-broad-from-our-rnaseq-subsets, bw_list_id=bw-hg19-Orlando2014-Jurkat
    threads: 2


        gtftk coverage  -x --inputfile out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Broad.bed --outputfile out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-broad-from-our-rnaseq-subsets_bw-hg19-Orlando2014-Jurkat.txt --chrom-info out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt --nb-proc 2 out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464990_20140211_733.spikein.hg19.bedgraph.bw out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1464999_20140509_1283.spikein.hg19.bedgraph.bw out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465003_20140509_1287.spikein.hg19.bedgraph.bw out/ucsc/bedGraphToBigWig_chrominfo-hg19/sort/_-k1,1_-k2,2n/tail/_-n+2/igvtools/tdftobedgraph/wget_interesting_samples_from_GSE60104/GSM1465019_20140211_746.spikein.hg19.bedgraph.bw &> out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-broad-from-our-rnaseq-subsets_bw-hg19-Orlando2014-Jurkat.log
        

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1359
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 2912
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 3194
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 3087
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1140
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1220
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1311
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 3013
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 2928
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 2696
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 3041
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 3117
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 2866
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 3148
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1874
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 2335
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, bw_list_id=bw-hg19-spikein-h3k4me3-inhibitors
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1175
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1448
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1598
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 3019
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2967
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 2530
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 3109
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 3211
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2871
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1819
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 954
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 2092
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule gtftk_coverage_extra_chrominfo_bed_single_bw:
    input: out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD4_TH91_H3K4me3_S010R5H1.bed, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.bw
    output: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-cd4-sharp/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.txt
    log: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-cd4-sharp/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.log
    jobid: 27
    reason: Missing output files: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-cd4-sharp/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.txt; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.bw, out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD4_TH91_H3K4me3_S010R5H1.bed, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt
    wildcards: tool=gtftk/coverage, extra=_-x, chrominfo_id=chrominfo-hg19, bed_list_id=bed-hg19-cd4-sharp, filler=ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3
    threads: 2


        gtftk coverage  -x --inputfile out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_CD4_TH91_H3K4me3_S010R5H1.bed --outputfile out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-cd4-sharp/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.txt --chrom-info out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt --nb-proc 2 out/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.bw &> out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-cd4-sharp/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.log
        

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 3122
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1230
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule gtftk_coverage_extra_chrominfo_bed_single_bw:
    input: out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_EC_TH91_H3K4me3_S010NDH1.bed, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.bw
    output: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-ec-sharp/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.txt
    log: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-ec-sharp/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.log
    jobid: 31
    reason: Missing output files: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-ec-sharp/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.txt; Input files updated by another job: out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_EC_TH91_H3K4me3_S010NDH1.bed, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.bw
    wildcards: tool=gtftk/coverage, extra=_-x, chrominfo_id=chrominfo-hg19, bed_list_id=bed-hg19-ec-sharp, filler=ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3
    threads: 2


        gtftk coverage  -x --inputfile out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_EC_TH91_H3K4me3_S010NDH1.bed --outputfile out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-ec-sharp/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.txt --chrom-info out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt --nb-proc 2 out/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.bw &> out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-ec-sharp/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.log
        

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 3181
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2829
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 2093
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 3295
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 3243
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2535
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1326
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 2679
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 2790
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 2275
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, bw_list_id=bw-hg19-spikein-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 2707
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 3049
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 3052
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 2704
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1356
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 3106
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1632
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2584
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2920
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 988
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 2294
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, bw_list_id=bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 2000
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1970
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 2881
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 2245
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-spikein-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1449
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 2423
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1092
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2597
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2414
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule gtftk_coverage_extra_chrominfo_bed_single_bw:
    input: out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD8_TH91_H3K4me3_S010S3H1.bed, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.bw
    output: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-cd8-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.txt
    log: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-cd8-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.log
    jobid: 13
    reason: Missing output files: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-cd8-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.txt; Input files updated by another job: out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.bw, out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD8_TH91_H3K4me3_S010S3H1.bed
    wildcards: tool=gtftk/coverage, extra=_-x, chrominfo_id=chrominfo-hg19, bed_list_id=bed-hg19-cd8-broad, filler=ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3
    threads: 2


        gtftk coverage  -x --inputfile out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD8_TH91_H3K4me3_S010S3H1.bed --outputfile out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-cd8-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.txt --chrom-info out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt --nb-proc 2 out/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.bw &> out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-cd8-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.log
        

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1001
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1276
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 3000
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2546
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 2451
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2578
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1645
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1920
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 2797
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 2572
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 3150
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 3051
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 2543
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 3272
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2599
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 2706
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1736
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2426
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 2770
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 3276
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 2421
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1678
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2567
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2918
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 3086
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 3188
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 3204
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 990
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 2766
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1049
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2409
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 2453
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 3045
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1172
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 3099
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1647
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2456
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1003
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:10 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 3193
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1816
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 2722
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 2541
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2407
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 3094
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1693
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2735
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1634
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 2859
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2569
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 2996
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1034
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 2935
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 3048
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 3110
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2689
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 2703
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2547
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 2401
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 3147
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 2676
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2596
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 945
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule r_compute_pausing_index_from_our_rnaseq:
    input: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/r/compute_pausing_index_in_broad_and_sharp_subsets_from_our_rnaseq/pi_boxplot.pdf, out/r/compute_pausing_index_in_broad_and_sharp_subsets_from_our_rnaseq/pi_boxplot.png, out/r/compute_pausing_index_in_broad_and_sharp_subsets_from_our_rnaseq/pi_genebodies_trim_500b_boxplot.png
    jobid: 12
    reason: Missing output files: out/r/compute_pausing_index_in_broad_and_sharp_subsets_from_our_rnaseq/pi_boxplot.png, out/r/compute_pausing_index_in_broad_and_sharp_subsets_from_our_rnaseq/pi_genebodies_trim_500b_boxplot.png; Input files updated by another job: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2152
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 2950
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2429
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 2905
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2872
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 3040
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 3142
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 2695
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2427
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 2561
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1508
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1589
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 3230
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 2708
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 3257
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 3053
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 3091
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2549
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 2593
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 2812
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 3226
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 3097
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 2403
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2459
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 3196
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1554
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 2432
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1876
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2438
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1540
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 3121
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 3157
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 3118
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 2816
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2566
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 2563
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 2981
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 2591
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 2184
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2406
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 2954
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2198
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1232
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2554
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2457
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 3213
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 2674
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2016
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 3210
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 3065
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2399
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1875
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 3104
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 2952
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 2442
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1956
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 2254
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, bw_list_id=bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 3189
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2965
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2448
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 2979
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 2865
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 2868
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2922
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1312
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 2984
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 2814
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1231
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 2531
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2397
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2827
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1372
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 2971
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 3241
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1827
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 3255
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 2938
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1174
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 3228
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1781
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2536
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 3202
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 3140
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1681
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 2925
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 3055
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1129
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1773
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 3183
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 3145
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 3247
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 2678
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1037
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 2857
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 2933
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 3260
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 3132
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 3050
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:11 2021]
rule gtftk_coverage_extra_chrominfo_bed_single_bw:
    input: out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_LC_TH91_H3K4me3_S010Q7H1.bed, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.bw
    output: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-lc-broad/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.txt
    log: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-lc-broad/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.log
    jobid: 29
    reason: Missing output files: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-lc-broad/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.txt; Input files updated by another job: out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.bw, out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_LC_TH91_H3K4me3_S010Q7H1.bed
    wildcards: tool=gtftk/coverage, extra=_-x, chrominfo_id=chrominfo-hg19, bed_list_id=bed-hg19-lc-broad, filler=ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3
    threads: 2


        gtftk coverage  -x --inputfile out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_LC_TH91_H3K4me3_S010Q7H1.bed --outputfile out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-lc-broad/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.txt --chrom-info out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt --nb-proc 2 out/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.bw &> out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-lc-broad/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.log
        

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 2705
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1137
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 2533
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1818
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1183
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 2798
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1323
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 2724
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 3112
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 3191
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1367
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 3137
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 2393
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1782
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 3178
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 3096
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 2903
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule gtftk_coverage_extra_chrominfo_bed_bw:
    input: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Sharp3.bed, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw
    output: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-sharp3-from-our-rnaseq-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt
    log: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-sharp3-from-our-rnaseq-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 15
    reason: Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Sharp3.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=gtftk/coverage, extra=_-x, chrominfo_id=chrominfo-hg19, bed_list_id=bed-hg19-jurkat-sharp3-from-our-rnaseq-subsets, bw_list_id=bw-hg19-spikein-h3k4me3-inhibitors
    threads: 2


        gtftk coverage  -x --inputfile out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Sharp3.bed --outputfile out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-sharp3-from-our-rnaseq-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt --chrom-info out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt --nb-proc 2 out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw &> out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-sharp3-from-our-rnaseq-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
        

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2396
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 3274
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1138
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 3287
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2011
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 2982
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:11 2021]
rule gtftk_coverage_extra_chrominfo_bed_bw:
    input: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Sharp1.bed, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw
    output: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-sharp1-from-our-rnaseq-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt
    log: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-sharp1-from-our-rnaseq-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 30
    reason: Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Sharp1.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=gtftk/coverage, extra=_-x, chrominfo_id=chrominfo-hg19, bed_list_id=bed-hg19-jurkat-sharp1-from-our-rnaseq-subsets, bw_list_id=bw-hg19-spikein-h3k4me3-inhibitors
    threads: 2


        gtftk coverage  -x --inputfile out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Sharp1.bed --outputfile out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-sharp1-from-our-rnaseq-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt --chrom-info out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt --nb-proc 2 out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw &> out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-sharp1-from-our-rnaseq-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
        

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 3101
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1967
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 3186
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2876
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 2914
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:11 2021]
rule gtftk_coverage_extra_chrominfo_bed_single_bw:
    input: out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD4_TH91_H3K4me3_S010R5H1.bed, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.bw
    output: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-cd4-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.txt
    log: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-cd4-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.log
    jobid: 10
    reason: Missing output files: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-cd4-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.txt; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.bw, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD4_TH91_H3K4me3_S010R5H1.bed
    wildcards: tool=gtftk/coverage, extra=_-x, chrominfo_id=chrominfo-hg19, bed_list_id=bed-hg19-cd4-broad, filler=ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3
    threads: 2


        gtftk coverage  -x --inputfile out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_CD4_TH91_H3K4me3_S010R5H1.bed --outputfile out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-cd4-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.txt --chrom-info out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt --nb-proc 2 out/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.bw &> out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-cd4-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.log
        

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 2911
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1507
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2781
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 2795
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2537
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 2391
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1004
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 2936
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 2768
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 2800
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1648
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2539
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 2720
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 3258
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2151
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 2787
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 3011
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2588
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 2264
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 3143
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 2582
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 3058
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 2998
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 3141
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 2743
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2691
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 3144
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1264
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1506
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2200
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2574
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 3198
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2595
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1497
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 3259
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 3256
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 3231
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1141
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 2400
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 2138
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 2972
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1543
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 2937
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 2934
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 2187
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1494
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1785
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 2314
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, bw_list_id=bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 2913
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 2141
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2150
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 2412
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1556
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 2560
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1908
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2418
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 2869
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 3248
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.bw, out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_LC_TH91_H3K4me3_S010Q7H1.bed, out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_LC_TH91_H3K4me3_S010Q7H1.bed
    output: out/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-lc-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-lc-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.log
    jobid: 2201
    benchmark: out/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-lc-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-lc-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.txt.gz; Input files updated by another job: out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_LC_TH91_H3K4me3_S010Q7H1.bed, out/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.bw, out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_LC_TH91_H3K4me3_S010Q7H1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_--referencePoint_center_-b_5000_-a_5000, bed_list_id=bed-hg19-lc-sharp-broad, filler=ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3
    threads: 2

computeMatrix  reference-point --referencePoint center -b 5000 -a 5000 --regionsFileName out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Broad/NM_Broad_LC_TH91_H3K4me3_S010Q7H1.bed out/sort/_-u/ln/updir/mw-tall/inp/Peaks_hg19_Mohammed/Sharp/NM_Sharp_LC_TH91_H3K4me3_S010Q7H1.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-lc-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-lc-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 2907
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 2215
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, bw_list_id=bw-hg19-spikein-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 2983
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 2980
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1081
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 2955
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 3056
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 2856
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2565
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1368
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:11 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 3209
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 3133
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 2590
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 3214
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2012
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 2817
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 3089
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 3119
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 3201
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 2864
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 2926
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1725
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2405
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 2771
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 3043
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1413
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 2698
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 2799
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 2796
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1265
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 2450
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1002
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1096
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2545
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2196
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1737
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 2910
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 3001
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 2225
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-spikein-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1552
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1093
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 2861
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1740
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 2915
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1646
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1909
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 3179
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2425
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 3102
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2057
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 2902
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1405
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 2788
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2558
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1188
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 2420
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 2552
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1588
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 2324
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 2867
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 3152
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2455
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2434
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 944
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1832
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2737
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 3187
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 3190
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:12 2021]
rule gtftk_coverage_extra_chrominfo_bed_bw:
    input: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Sharp2.bed, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw
    output: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-sharp2-from-our-rnaseq-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt
    log: out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-sharp2-from-our-rnaseq-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 24
    reason: Input files updated by another job: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw, out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Sharp2.bed
    wildcards: tool=gtftk/coverage, extra=_-x, chrominfo_id=chrominfo-hg19, bed_list_id=bed-hg19-jurkat-sharp2-from-our-rnaseq-subsets, bw_list_id=bw-hg19-spikein-h3k4me3-inhibitors
    threads: 2


        gtftk coverage  -x --inputfile out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_Sharp2.bed --outputfile out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-sharp2-from-our-rnaseq-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt --chrom-info out/gunzip/to-stdout/wget/http/hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt --nb-proc 2 out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bw out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bw &> out/gtftk/coverage_-x_chrominfo-hg19_bed-hg19-jurkat-sharp2-from-our-rnaseq-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
        

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 2540
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 2049
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 3277
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 3212
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:12 2021]
localrule ln_alias:
    input: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.bw
    output: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw
    jobid: 3322
    reason: Missing output files: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw; Input files updated by another job: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.bw
    wildcards: id=sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw
    priority: 10

ln -srf 'out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186665_H3K79me2.bw' out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw

[Sat Apr 17 13:59:12 2021]
localrule ln_alias:
    input: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.bw
    output: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw
    jobid: 3333
    reason: Missing output files: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw; Input files updated by another job: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.bw
    wildcards: id=sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw
    priority: 10

ln -srf 'out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_SRX2636361_H3K36me3.bw' out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw

[Sat Apr 17 13:59:12 2021]
localrule ln_alias:
    input: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.bw
    output: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw
    jobid: 3321
    reason: Missing output files: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw; Input files updated by another job: out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.bw
    wildcards: id=sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw
    priority: 10

ln -srf 'out/deepTools/bamCoverage_--binSize_20_--minMappingQuality_0_--normalizeUsing_RPKM/samtools/index/samtools/sort/samtools/view_sam_to_bam_-q_30/bowtie2/se_hg19/sickle/se_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/DND-41_SRX186659_H3K36me3.bw' out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1290
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1570
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1069
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-cd8-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--whatToShow_cph/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-cd8-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--whatToShow_cph/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-cd8-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--whatToShow_cph/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-cd8-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.log
    jobid: 5
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--whatToShow_cph/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-cd8-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--whatToShow_cph/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-cd8-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-cd8-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-cd8-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-cd8-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--whatToShow_cph/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-cd8-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--whatToShow_cph/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-cd8-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--whatToShow_cph/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-cd8-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP8_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 534
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1445
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1055
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1594
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 516
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 2157
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1329
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 557
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1592
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 303
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 785
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1515
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1300
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 380
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 407
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1944
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 660
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 687
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 2159
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 163
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 505
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1973
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 837
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 948
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1513
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 796
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 950
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 814
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1699
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 2089
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 926
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1713
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1934
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 556
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1938
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 554
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 2101
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1984
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1089
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 645
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1088
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1421
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 976
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1160
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1658
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1999
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 560
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1778
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1478
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 2055
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1472
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1192
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1206
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1807
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1163
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 2116
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1850
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1836
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1411
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1134
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 2122
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 840
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1355
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1620
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1804
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 2065
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 365
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1732
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1733
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1340
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1294
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1457
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 834
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 836
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 978
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2036
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 2192
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 416
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 994
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 2073
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1376
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1976
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1195
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 2158
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1623
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1545
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 379
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 418
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1720
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 264
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 2050
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 698
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 124
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1076
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1406
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 979
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 659
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 2189
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1514
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1839
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1638
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1429
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 2020
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1332
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1548
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 696
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1622
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1392
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1640
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 683
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1201
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 2190
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 842
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1079
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1119
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 2088
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 369
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 561
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1959
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 655
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1111
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 987
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 918
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1202
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1687
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1271
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1943
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1806
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1240
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1884
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1162
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1299
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1915
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1846
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1043
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1562
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1631
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 375
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 841
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 649
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1315
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1444
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:12 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 562
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1763
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1723
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 996
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 403
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1845
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1961
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1546
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1479
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1487
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1536
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 995
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 294
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 414
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 2147
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1933
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1425
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1123
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1914
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 949
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1291
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1702
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 537
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1685
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1683
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1014
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 123
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 263
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 817
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1935
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1041
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1039
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1058
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1270
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1767
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 2069
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1289
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1503
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 694
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 2180
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2131
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 2123
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1639
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 154
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1317
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1211
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 651
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1115
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1991
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1061
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1056
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 134
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1269
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1669
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1401
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 2053
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 673
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 283
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1610
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2037
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1844
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1891
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 782
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1298
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 114
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 2100
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1749
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 776
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1893
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1382
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1484
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1104
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1748
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2128
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 2026
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1249
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1105
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 496
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1456
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 254
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 502
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1942
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1200
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1247
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 143
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1393
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 966
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-lc-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--whatToShow_cph/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-lc-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--whatToShow_cph/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-lc-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--whatToShow_cph/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-lc-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.log
    jobid: 25
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--whatToShow_cph/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-lc-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--whatToShow_cph/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-lc-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-lc-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-lc-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-lc-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--whatToShow_cph/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-lc-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--whatToShow_cph/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-lc-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--whatToShow_cph/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-lc-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_LC_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1409
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 393
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 274
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1913
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1025
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 2045
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1700
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1705
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1759
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1855
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 371
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1347
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1568
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 133
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1979
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1157
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 2019
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2083
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 784
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1245
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 410
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 538
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 539
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1838
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 533
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 779
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1888
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 508
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1617
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 646
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 522
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1885
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 648
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 368
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1241
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 802
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 973
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 788
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1244
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 813
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 499
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1194
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 819
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 504
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1889
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 690
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 818
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1439
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1375
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1335
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1801
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 924
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 273
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 951
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1907
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1176
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1191
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 551
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 2030
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 524
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 820
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 2027
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1026
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1929
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1476
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 938
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1133
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 361
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 801
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1342
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1345
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1704
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 980
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1018
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 664
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 2091
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1337
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 384
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1981
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1662
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1447
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1986
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1181
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1989
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 521
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1624
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1777
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 641
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1582
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1285
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 2120
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1670
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 540
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1383
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 804
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1386
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1835
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 831
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1820
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-ec-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--whatToShow_cph/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-ec-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--whatToShow_cph/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-ec-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--whatToShow_cph/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-ec-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.log
    jobid: 34
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--whatToShow_cph/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-ec-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--whatToShow_cph/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-ec-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-ec-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-ec-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-ec-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--whatToShow_cph/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-ec-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--whatToShow_cph/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-ec-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--whatToShow_cph/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-ec-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_EC_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1595
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1263
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1574
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1870
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 153
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1519
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1486
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 833
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 997
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 94
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 93
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 546
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1063
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1246
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 789
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1668
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 144
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 284
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1024
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:13 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 509
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1890
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1707
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 826
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 233
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1859
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 234
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 553
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1641
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2130
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 2163
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 293
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 930
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 113
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1226
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1837
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 517
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 835
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1779
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1744
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1331
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 925
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 808
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1257
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 927
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1517
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1901
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1571
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 2161
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 528
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1569
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1975
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1135
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1100
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 555
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 797
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1344
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 253
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1316
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1087
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1522
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 2078
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 2074
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1262
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1198
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1899
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 2066
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 2146
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1399
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1521
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1547
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1815
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 984
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1761
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1630
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 2182
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1714
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1070
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1117
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1628
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1538
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 986
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 2191
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1171
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 2043
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 2165
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1502
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1255
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1842
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1422
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1906
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1430
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1434
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1731
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 2166
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1960
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1998
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2127
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1708
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1664
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 923
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1007
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 778
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1799
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1825
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1682
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 54
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1802
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1309
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1011
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 386
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 965
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 374
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1575
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1754
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 695
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1841
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 668
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1618
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1498
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1616
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 2142
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 974
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 972
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 388
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1110
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 415
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1197
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 931
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 654
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1609
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1655
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 666
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1953
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1155
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 194
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1038
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1158
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1651
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1064
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1354
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1020
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1567
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1483
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 498
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1823
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1590
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1728
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 928
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 968
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 2008
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1054
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1747
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1608
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1306
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1800
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1684
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1222
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1040
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1866
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1156
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1950
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1103
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1698
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 964
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1364
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1612
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1254
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1572
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1084
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 946
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1179
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 2023
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1775
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 193
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 370
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 2168
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 793
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1378
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1453
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1224
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1607
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1471
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 536
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1912
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1438
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 389
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1012
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 791
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 678
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1900
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1072
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1656
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 511
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 398
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1256
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1716
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 669
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1268
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 816
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2082
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1868
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 2115
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 513
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 2022
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 2097
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1524
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 963
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 53
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 650
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1379
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1131
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 519
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 164
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1168
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1330
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1686
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 419
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1101
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 494
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 514
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1068
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1384
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 947
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 412
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1225
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 642
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:14 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 420
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1130
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 552
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1774
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 832
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 700
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 362
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1869
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 692
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1712
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1591
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 2028
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 794
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1745
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 699
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 774
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1812
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1974
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1042
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 304
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 799
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1015
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 535
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 2113
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 387
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2080
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1743
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2126
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1334
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 421
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1215
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1523
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1022
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1577
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1319
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 786
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1010
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 691
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1932
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 357
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1593
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 366
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 2134
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 503
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1793
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1676
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 541
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 821
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 783
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1149
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 637
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1032
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-cd4-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--whatToShow_cph/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-cd4-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--whatToShow_cph/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-cd4-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--whatToShow_cph/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-cd4-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.log
    jobid: 17
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--whatToShow_cph/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-cd4-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--whatToShow_cph/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-cd4-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-cd4-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-cd4-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-cd4-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--whatToShow_cph/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-cd4-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--whatToShow_cph/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-cd4-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--whatToShow_cph/deepTools/computeMatrix_reference-point_--referencePoint_center_-b_5000_-a_5000_bed-hg19-cd4-sharp-broad/ln/alias/sst/all_samples/hg19/bw/TH91_SP4_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1288
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 411
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1490
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1654
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1963
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 933
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 506
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1666
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 2167
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 701
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1099
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1978
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1482
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 667
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1436
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1659
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 815
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1469
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1533
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1387
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1125
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1009
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 688
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 693
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1410
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1272
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1177
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 686
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 635
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 2162
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1904
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 967
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1124
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1223
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1768
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 2096
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1867
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1452
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1611
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1518
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1260
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 355
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 406
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1821
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1916
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 2054
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 413
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 408
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2177
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1769
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1653
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 2031
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1883
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1905
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 939
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1308
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1303
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1214
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 697
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 977
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 971
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1766
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1216
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 2188
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 934
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1165
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 544
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1427
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1675
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1031
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 2071
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 824
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1578
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1809
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1544
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1860
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1122
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1621
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1615
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 417
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1947
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1952
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1858
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1239
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1261
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1583
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 829
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1016
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1710
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 392
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1146
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 775
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 656
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 2042
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1336
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1928
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 529
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1939
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 828
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1927
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 381
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1667
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1985
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1493
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 682
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--yMax_2_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--yMax_2_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--yMax_2_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 16
    benchmark: out/deepTools/plotHeatmap_--yMax_2_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--yMax_2_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--yMax_2_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--yMax_2_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--yMax_2_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --yMax 2 --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--yMax_2_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 402
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1023
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1341
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 2137
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 661
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1283
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 548
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1295
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1398
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 495
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1980
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 376
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1284
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 809
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1790
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 672
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1066
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1660
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 549
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2173
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 550
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 795
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 400
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1851
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1454
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1432
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1059
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 839
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1301
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 2099
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1455
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 559
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1945
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1703
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 2076
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 2098
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1207
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 515
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 680
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 830
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1529
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 358
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1065
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 43
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 961
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1537
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 2009
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 532
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:15 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 523
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1663
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1145
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1400
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 919
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1563
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 2044
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1789
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1019
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 803
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 812
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 2181
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1365
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1605
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 183
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1709
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 638
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 647
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2175
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 675
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 213
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1853
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 2114
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 922
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1286
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1990
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1871
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1722
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1078
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1227
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1346
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1930
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1470
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1566
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1209
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 73
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1531
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 367
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 395
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1614
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 391
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1946
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1437
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1118
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1085
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1940
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 2169
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1248
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 2068
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 74
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 526
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 2136
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 520
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 790
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1446
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1339
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 184
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 810
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1385
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 530
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 2029
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1983
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 510
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 2090
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 44
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1492
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 800
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1424
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 806
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 214
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1892
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1525
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1296
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1762
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1729
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1302
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 671
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 970
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1755
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2081
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1576
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1499
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1164
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 501
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 920
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 399
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 822
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1977
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 941
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 401
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 422
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1750
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1813
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1606
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 2124
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 244
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 104
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 962
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1169
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1480
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1106
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 702
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 681
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 542
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 679
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1333
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1564
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1585
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 781
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1808
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 2143
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 932
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1441
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1677
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1894
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 2129
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1795
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1361
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1798
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 2174
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 2075
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1338
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 2035
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1057
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1982
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1391
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1701
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1431
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1530
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1154
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1485
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 2005
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1151
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1250
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1033
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2085
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 2111
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1242
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1751
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1674
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1203
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 636
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1148
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1381
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 497
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 639
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1613
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1408
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 935
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1199
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1843
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 969
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1579
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 2052
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 359
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 777
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 2025
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1792
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1847
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 356
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1030
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1886
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1107
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1467
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 644
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1715
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1501
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1292
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 2119
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1746
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1109
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 689
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1721
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 670
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1560
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1584
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 103
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1349
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 243
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1993
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 940
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 916
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 390
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1077
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 409
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1753
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1475
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1936
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1102
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 2145
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log
    jobid: 1071
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 364
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 507
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1388
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1756
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1253
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 798
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 823
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1539
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 353
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1362
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 314
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1717
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1237
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 643
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 2144
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1147
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1852
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 2164
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:16 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1428
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1008
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 684
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 224
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 405
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1243
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 354
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 2135
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1887
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 685
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 634
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1491
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 84
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 404
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 2072
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1652
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1520
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1208
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1791
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1881
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1500
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 363
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1073
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 174
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 633
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 543
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 2006
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 2183
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 518
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1112
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1897
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 787
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 2032
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 662
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1474
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1053
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1625
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 2121
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1516
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 985
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1108
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1951
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1426
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1758
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1395
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 2067
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1352
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 2077
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 676
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1997
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2176
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 203
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 493
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 2170
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1526
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 63
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 773
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log
    jobid: 396
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1353
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1532
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1996
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1433
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1423
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1307
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1752
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1114
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 2039
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 2070
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1629
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1477
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 2160
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1697
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 382
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 981
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 2118
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 780
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1706
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 838
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2034
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 2051
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1468
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 674
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1958
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1287
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1473
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1898
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 2193
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1152
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 827
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 531
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 663
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1132
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 807
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1377
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1170
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 1559
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1854
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1861
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1161
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 373
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 658
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 652
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 653
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 378
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 512
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log
    jobid: 915
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1210
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log
    jobid: 1217
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 372
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log
    jobid: 792
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1814
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 2021
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 1805
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1193
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log
    jobid: 811
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1776
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log
    jobid: 383
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 547
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1549
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1796
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log
    jobid: 1931
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 2117
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log
    jobid: 1060
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 527
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 2112
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1314
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1390
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1407
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log
    jobid: 394
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1062
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log
    jobid: 558
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 500
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1394
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1360
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1013
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 223
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1824
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1962
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 173
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1528
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1992
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1917
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1252
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1661
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1086
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1730
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1017
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1273
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1348
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1896
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 2172
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 1988
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 313
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1318
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log
    jobid: 1180
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log
    jobid: 83
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1657
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 2004
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1882
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2038
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1150
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 397
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1178
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 665
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 917
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 1637
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 1440
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 2007
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 2024
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 204
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 805
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 640
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1636
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 1565
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1760
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1848
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1196
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1293
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1027
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 825
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1797
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 377
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log
    jobid: 1671
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 657
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1937
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1840
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 545
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 1153
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log
    jobid: 1116
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log
    jobid: 1204
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log
    jobid: 360
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log
    jobid: 921
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log
    jobid: 992
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 525
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log
    jobid: 64
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1380
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log
    jobid: 2084
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log
    jobid: 1363
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log
    jobid: 993
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log
    jobid: 1822
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log
    jobid: 1794
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log
    jobid: 385
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log
    jobid: 1561
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log
    jobid: 677
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log
    jobid: 1238
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.log

[Sat Apr 17 13:59:17 2021]
localrule meta_broad_tall_rev3_q4_spikein_single:
    input: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, 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out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, 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out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/deepTools/spikeIn_bamCoverage_BDGP6/samtools/sam_to_bam_bai_-q_30/bowtie2/pe_hg19/sickle/pe_-t_sanger_-q_20/ln/alias/sst/all_samples/fastq/Loucy_DMSO_24H_H3K4me3.pdf

[Sat Apr 17 13:59:17 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 2272
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 2762
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 2242
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:17 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 2847
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 2992
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 2717
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 2332
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 2306
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-h3k36me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 3268
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 2228
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 3222
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 2893
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 3153
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 3307
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 2671
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 3062
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 2296
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-h3k36me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 2221
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-h3k36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 2342
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 2232
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 2946
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 2282
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 2808
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 3031
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 3008
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 2287
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 2831
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 2778
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 3284
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 2347
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 2257
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 2223
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 2214
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 2298
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 3291
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 2317
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 3238
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 2740
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 3169
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 2311
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-h3k36me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 2877
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 2247
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 3015
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 2824
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 2241
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-h3k36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 2962
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 2273
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 3016
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 2243
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 2333
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 2256
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-h3k36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 2739
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 2318
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 2878
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 3077
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 2686
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 2331
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-h3k36me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 3292
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 2732
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 2227
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 2993
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 2266
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-h3k36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 2343
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 2233
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 2283
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 2832
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 2809
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 2288
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 2281
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-h3k36me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 2947
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 2271
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-h3k36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 2348
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 2670
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 2316
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-h3k36me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 2755
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 3223
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 2341
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-h3k36me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 2258
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 2222
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 3154
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 3269
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 2326
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-h3k36me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 2213
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 2297
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 2716
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 2248
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 2763
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 2970
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 2276
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-h3k36me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 2246
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-h3k36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 2336
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-h3k36me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 2253
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 2302
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 3131
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 2321
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-h3k36me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 3123
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 3246
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 2328
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 2924
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 2693
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 3038
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 3084
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 3177
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 2292
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 2217
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 2263
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 2346
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-h3k36me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 2786
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 2236
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-h3k36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 2286
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-h3k36me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 2291
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-h3k36me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 2278
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 2268
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 2351
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-h3k36me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 3200
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 2709
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 3054
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 2313
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 2855
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 2338
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 3107
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 2261
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-h3k36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 2901
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 2323
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 2307
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 3100
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 2251
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-h3k36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 2238
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 2801
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 2252
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 2303
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 2900
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 3192
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 2327
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 2231
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-h3k36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 3146
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 2854
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 3261
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 3108
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 2939
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 3199
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 2218
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 2293
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 2262
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 2985
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 2785
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 2277
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 3176
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 2916
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 2267
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 2337
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 2226
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-h3k36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 2312
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 3085
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 3215
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 2216
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-h3k36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 2301
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-h3k36me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 2923
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 2694
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 3039
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 2322
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 2870
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 --unscaled3prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 3130
    benchmark: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    threads: 2

computeMatrix  scale-regions --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Broad.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp1.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp2.bed out/r/extract_control_sharp_subsets_from_our_rnaseq/NM_genes_associated_with_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 2308
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2_length_gt_1500b_trim_500b_at_TSS_TES.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3_length_gt_1500b_trim_500b_at_TSS_TES.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 3245
    benchmark: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_reference-point_-b_5000_-a_5000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    threads: 2

computeMatrix  reference-point -b 5000 -a 5000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw --outFileName out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 3061
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --unscaled3prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_SingleBw_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 2969
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz; Input files updated by another job: out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, filler=ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    threads: 2

computeMatrix  scale-regions -b 500 -a 500 --unscaled5prime 500 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_computeMatrix_extra:
    input: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed
    output: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    log: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 2237
    benchmark: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz; Input files updated by another job: out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw, out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed, out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw, out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed
    wildcards: tool=deepTools/computeMatrix, extra=_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000, bed_list_id=bed-hg19-jurkat-broad-and-sharp-subsets, bw_list_id=bw-hg19-broad-tall-rev3-q4
    threads: 2

computeMatrix  scale-regions -b 5000 -a 5000 --unscaled5prime 5000 -m 20000 --maxThreshold 1000 --regionsFileName out/r/extract_control_sharp_subsets_from_Atak2013/NM_Broad.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp1.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp2.bed out/r/extract_control_sharp_subsets_from_Atak2013/NM_Sharp3.bed --scoreFileName out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.bw out/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.bw out/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bw --outFileName out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --numberOfProcessors 2 &> out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1228
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 983
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1672
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1481
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 62
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1189
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 286
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 271
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1504
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 45
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1327
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1143
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 127
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 80
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 187
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1120
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 975
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1558
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1994
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 2010
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1351
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1297
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1948
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 72
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 210
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1488
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 2132
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 70
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 212
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1941
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1304
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1350
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1995
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1366
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1619
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1764
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 914
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 47
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 267
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1787
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 220
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1971
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 185
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 146
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 2148
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1833
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 131
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 2125
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 202
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1627
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1028
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1872
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1803
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1320
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1895
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 307
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 222
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 2017
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 2086
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 96
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1412
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:18 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 260
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 237
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1458
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 241
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1741
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1465
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 75
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1166
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 171
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1918
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1466
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 306
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1075
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 87
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 140
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 285
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 280
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 145
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 227
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 166
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1719
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 2110
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 311
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1274
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 2109
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 215
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1810
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1097
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 101
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 2102
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 2056
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 120
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 97
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 236
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1442
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 167
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1251
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1373
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 82
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1964
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1159
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1695
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 320
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 302
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 56
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1649
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1604
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1389
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 195
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 312
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 90
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1834
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1757
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 2156
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 191
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 277
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 100
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 275
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 65
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1205
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 205
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1849
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 135
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 137
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 240
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1512
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 51
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 172
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1190
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 230
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 55
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1113
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 960
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 2033
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1005
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 196
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1051
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 162
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 180
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 252
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 296
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 170
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 111
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1673
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 91
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1281
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 95
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 998
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 297
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 206
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 42
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 232
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 291
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1987
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 2194
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 115
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1972
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 175
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 952
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 292
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 110
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1044
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1489
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 216
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1879
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 165
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 161
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 301
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 76
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 305
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1235
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 250
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 2133
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1596
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 315
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 152
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1688
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1343
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 255
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1550
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1328
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 182
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 92
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1642
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 157
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 151
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 66
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1925
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 235
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 231
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 251
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1029
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 310
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 112
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 156
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 86
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1926
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 46
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1557
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 181
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 126
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 50
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1949
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1136
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 117
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 261
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 150
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 247
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1396
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1665
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1419
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 245
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 105
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 2063
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 2040
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1021
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 107
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 290
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 121
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1780
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 190
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1305
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 257
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 913
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 266
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 41
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1282
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 226
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 186
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 160
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 2179
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1443
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1420
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 130
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 262
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1121
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 246
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 85
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 2018
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1650
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 242
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1696
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 142
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 116
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 71
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 197
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 192
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 125
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 265
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 52
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 57
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 256
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 211
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1052
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 282
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 102
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1006
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1374
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 225
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 106
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1765
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 122
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 270
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 2064
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 300
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1535
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 2087
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1857
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1511
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1534
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1167
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 281
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 81
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1212
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 929
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:19 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1734
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 937
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 60
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 2171
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 201
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 177
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1902
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1788
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 287
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 207
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1711
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1067
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 147
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 61
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 317
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1258
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 67
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1144
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1527
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 200
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1581
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1573
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1090
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1856
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 221
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 141
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 2155
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 2178
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1811
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1213
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1259
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1880
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 316
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1718
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 132
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1742
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 155
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1435
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1397
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 217
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 982
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1182
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 276
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1603
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1580
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 936
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 959
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 136
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 77
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1626
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 1826
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 2041
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log
    jobid: 2079
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log
    jobid: 295
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1098
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log
    jobid: 1074
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log
    jobid: 272
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log
    jobid: 176
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf; Input files updated by another job: out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1236
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:20 2021]
rule deepTools_plotHeatmap_extra:
    input: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    output: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed
    log: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log
    jobid: 1903
    benchmark: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.benchmark.tsv
    reason: Missing output files: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf; Input files updated by another job: out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz
    wildcards: tool=deepTools/plotHeatmap, extra=_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none, filler=deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2
    priority: 2

plotHeatmap --matrixFile out/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.txt.gz --outFileName out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf --outFileSortedRegions out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.bed  --colorList '#313695,#B6DFEC,#FFF6B1,#F67C4A,#A70226' --heatmapWidth 6 --whatToShow 'plot, heatmap and colorbar' --legendLocation none &> out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.log

[Sat Apr 17 13:59:20 2021]
localrule meta_broad_tall_rev3_q4:
    input: out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, 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out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-no-h3k4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets_bw-hg19-spikein-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-spikein-jurkat-h3k4me3-inhibitors.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets_bw-hg19-broad-tall-rev3-q4.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets_bw-hg19-broad-tall-rev3-q4-h3k36me3.pdf

[Sat Apr 17 13:59:20 2021]
localrule meta_broad_tall_rev3_q4_single:
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out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, 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out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, 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out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, 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out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536543_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRR5338727_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186659_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR11783980_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_SRX2636361_H3K36me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1057275_CDK7.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR1536561_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_OCIR_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536556_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_RY_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PM_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_PBIT_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/DND-41_SRX186665_H3K79me2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_DMSO_24H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_--unscaled3prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Loucy_PBIT_5H_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--unscaled3prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_Ctrl_SRR1536552_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_500_-a_500_--unscaled5prime_500_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_EPZ_SRR1536572_H3K4me3.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_scale-regions_-b_5000_-a_5000_--unscaled5prime_5000_-m_20000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-from-our-rnaseq-genes-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR2157609_Pol2.pdf, out/deepTools/plotHeatmap_--colorList_blueCyanYellowOrangeRed_--heatmapWidth_6_--whatToShow_cph_--legendLocation_none/deepTools/computeMatrix_reference-point_-b_5000_-a_5000_--maxThreshold_1000_bed-hg19-jurkat-broad-and-sharp-length-gt-1500b-trim-500b-at-TSS-TES-subsets/ln/alias/sst/all_samples/hg19/bw/Jurkat_SRR231122_DNaseI.pdf

Job counts:
	count	jobs
	1	bowtie2_build
	20	bowtie2_paired_end_extra
	17	bowtie2_single_end_extra
	15	cat
	27	deepTools_bamCoverage_extra
	928	deepTools_computeMatrix_SingleBw_extra
	140	deepTools_computeMatrix_extra
	2133	deepTools_plotHeatmap_extra
	10	deepTools_spikeIn_bamCoverage
	1	gtftk_convert_ensembl
	12	gtftk_coverage_extra_chrominfo_bed_bw
	8	gtftk_coverage_extra_chrominfo_bed_single_bw
	1	gtftk_get_5p_3p_coords
	1	gtftk_select_by_key_key_value
	31	gunzip_extra
	4	igvtools_tdftobedgraph
	87	ln_alias
	58	ln_srf_parent_dir
	1	meta_broad_tall_rev3_q4
	1	meta_broad_tall_rev3_q4_single
	1	meta_broad_tall_rev3_q4_spikein_single
	1	r_compute_pausing_index
	1	r_compute_pausing_index_from_our_rnaseq
	1	r_extract_control_sharp_subsets_from_Atak2013
	1	r_extract_control_sharp_subsets_from_our_rnaseq
	33	samtools_index
	20	samtools_sam_to_bam_bai_extra
	27	samtools_sort_extra
	27	samtools_view_sam_to_bam_extra
	15	sickle_pe_extra
	18	sickle_se_extra
	16	sort_extra
	16	sra_tools_fastq_dump_se_extra
	1	star_build_index
	5	star_pe_extra
	1	star_se_extra
	2	subread_featureCounts_extra
	4	tail_extra
	1	tar_xvzf_igenome
	4	ucsc_bedGraphToBigWig
	32	wget_protocol
	3723
This was a dry-run (flag -n). The order of jobs does not reflect the order of execution.
